Low-pass genome sequencing: a validated method in clinical cytogenetics
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ORIGINAL INVESTIGATION
Low‑pass genome sequencing: a validated method in clinical cytogenetics Matthew Hoi Kin Chau1,2,3 · Huilin Wang4 · Yunli Lai5,6 · Yanyan Zhang1,2 · Fuben Xu5,6 · Yanqing Tang5,6 · Yanfang Wang4 · Zihan Chen2 · Tak Yeung Leung1,2,7 · Jacqueline Pui Wah Chung1 · Yvonne K. Kwok1,2 · Shuk Ching Chong3,7,8 · Kwong Wai Choy1,2,3,7 · Yuanfang Zhu4 · Likuan Xiong4 · Weihong Wei5,6 · Zirui Dong1,2,3 Received: 11 March 2020 / Accepted: 18 May 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract Clinically significant copy-number variants (CNVs) known to cause human diseases are routinely detected by chromosomal microarray analysis (CMA). Recently, genome sequencing (GS) has been introduced for CNV analysis; however, sequencing depth (determined by sequencing read-length and read-amount) is a variable parameter across different laboratories. Variating sequencing depths affect the CNV detection resolution and also make it difficult for cross-laboratory referencing or comparison. In this study, by using data from 50 samples with high read-depth GS (30×) and the reported clinically significant CNVs, we first demonstrated the optimal read-amount and the most cost-effective read-length for CNV analysis to be 15 million reads and single-end 50 bp (equivalent to a read-depth of 0.25-fold), respectively. In addition, we showed that CNVs at mosaic levels as low as 30% are readily detected, furthermore, CNVs larger than 2.5 Mb are also detectable at mosaic levels as low as 20%. Herein, by conducting a retrospective back-to-back comparison study of low-pass GS versus routine CMA for 532 prenatal, miscarriage, and postnatal cases, the overall diagnostic yield was 22.4% (119/532) for CMA and 23.1% (123/532) for low-pass GS. Thus, the overall relative improvement of the diagnostic yield by low-pass GS versus CMA was ~ 3.4% (4/119). Identification of cryptic and clinically significant CNVs among prenatal, miscarriage, and postnatal cases demonstrated that CNV detection at higher resolutions is warranted for clinical diagnosis regardless of referral indications. Overall, our study supports low-pass GS as the first-tier genetic test for molecular cytogenetic testing.
Introduction Matthew Hoi Kin Chau, Huilin Wang and Yunli Lai contributed equally. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00439-020-02185-9) contains supplementary material, which is available to authorized users. * Zirui Dong [email protected] 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
Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
4
Department of Center Laboratory, Maternal‑Fetal Medicine Institute, Shenzhen Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Baoan Maternity and Child Health Hospital Affiliated to Ji
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