Doctor DONG Zirui Elvis

Assistant Professor,
Department of Obstetrics and Gynaecology, CUHK
Committee Member, Experiential Learning & Global Engagement Committee, Lee Woo Sing College, CUHK
Member of the Run Run Shaw Science Building (RRSSB) Management Committee, CUHK
Associate Researcher [副研究員],
Shenzhen Research Institute, CUHK

Research Theme

Genetics & Genomics

Biography

I developed low-pass genome sequencing assays for detecting balanced/unbalanced structural variants (SVs), and demonstrated its feasibility and superiority on the detection scope and resolution to routine standard care. It has been recognized and recommended by the American College of Medical Genetics and Genomics for detecting germline SVs clinically, and we demonstrate SVs’ pathogenicity by gene disruption/dysregulation. It leads to 29 articles in peer-reviewed journals, 17 of which I am the first/co-first/corresponding author (with 7 in top 10% of the category of Genetics and Heredity). The first landmark paper has ~145 citations. Our studies have been presented at 23 international, national, or regional conferences. Currently, I serve as Principal Investigator for 9 external (3 HMRF, 1 ITF, 2 NSFC) and 3 internal grants, and as co-PI for a CRF. Furthermore, we filed two international patents for the analytical pipelines and licensed to two companies for services.

I am also serving as a guest editor in two peer-reviewed journals, and as a committee member for two professional committees on clinical genetics.

Recently, we established Temporal Expression during Development Database (TEDD) to facilitate researchers understand cell-type and timepoint specific expression pattern during prenatal and early postnatal development by single-cell analysis for disease investigation.

Education

Ph.D. (CUHK, 2017)
MSc (CUHK, 2013)
BEng (SCUT, 2009)

Research Interests

Development and implementation of low-pass Genome Sequencing (GS) for identifying clinically significant copy-number variants (CNVs), chromosomal structural rearrangements (SVs, e.g., balanced translocations and inversions) and absence of heterozygosity (AOHs, e.g., uniparental disomy and parental consanguinity) in prenatal, paediatrics and adult diseases
Deciphering the spectrum of structural variants and investigation on its impact to human diseases (fetal ultrasound anomalies and male infertility) including alternation in 3D organization (with Hi-C/4C) and gene expression aberration (with multi-omics: single-cell RNA-seq, ATAC-seq and ChIP-seq)
Study on the potential repair mechanism of structural variants (e.g., chromosome insertion and chromothripsis) by establishing different factors induced cell models and analysis with in-house single-cell mate-pair sequencing.

Qualifications

Certificate of Clinical Genetic Counseling (#YC201602183), Chinese Board of Genetic Counseling, Capacity Building and Continuing Education Center, National Health and Family Planning Commission of China

Honorary Appointment

Adjunct Assistant Research Fellow, Center for Reproductive Medicine, Shandong University, China
Visiting Scholar, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA (Under supervision of Prof. Cynthia C. MORTON)

Editorship

Guest editor. Genes (Research Topic: Novel Insights into Prenatal Genetic Testing), 01/12,2021-present
Guest associate editor, Frontiers in Genetics (Research Topic: Chromosome Structural Variants: Epidemiology, Identification and Contribution to Human Diseases), 01/07,2020-present
Review Editor, Editorial Board of Genetics of Common and Rare Diseases, Frontiers in Pediatrics and Frontiers in Genetics, 01/11/2020-present

Professional Service

Committee Member, Professional Committee on Reproductive and Genetic Management, Association for Medical Education of Guangdong Province, China, 03/2023
Committee Member, Clinical Genetics and Genetic Counseling Board (CGGCB), Shanghai Society of Genetics, China, 05/2020

Academic Engagement

Currently, I am supervising two PhD students.

Patent

DONG Z, CHOY KW, LI K, CHAU MHK. METHODS OF USING ALGORITHMIC ANALYSIS TO DETERMINE MATERNITY, PATERNITY, OR PARENTAGE AND COMPUTER SYSTEMS FOR IMPLEMENTATION THEREOF. U.S. Provisional Patent Application No. 63/504,845; filed May 30, 2023
CHOY KW, DONG Z, CAO Y, YANG Z. Methods for detecting absence of heterozygosity by low-pass genome sequencing. US Provisional Application no: 62/894,491, filed on 08/30/2019
CHOY KW, DONG Z, CAO Y, YANG Z. Methods for detecting absence of heterozygosity by low-pass genome sequencing. US Non-Provisional Application no. 17/005,569, filed on 28/08/2020
CHOY KW, DONG Z, CAO Y, YANG Z. Methods for detecting absence of heterozygosity by low-pass genome sequencing. PCT Application no. PCT/CN2020/111016, filed on 25/08/2020

Publications

*co-first; #corresponding

Mate-pair genome sequencing reveals structural variants for idiopathic male infertility

Dong Z,# Qian J, Law TSM, Chau MHK, Cao Y, Xue S, Tong S, Zhao Y, Kwok YK, Ng K, Chan DYL, Chiu PKF, Ng CF, Chung CHS, Mak JSZM, Leung TY, Chung JPW, Morton CC, Choy KW

Hum Genet. 2023 Mar;142(3):363-377

TEDD: a database of temporal gene expression patterns during multiple developmental periods in human and model organisms

Zhou Z, Tan C, Chau MHK, Jiang X, Ke Z, Chen X, Cao Y, Kwok YK, Bellgard M, Leung TY, Choy KW, Dong Z#

Nucleic Acids Res. 2023 Jan 6;51(D1):D1168-D1178

Low-pass genome sequencing-based detection of paternity: validation in clinical cytogenetics

Li K, Zhao Y, Chau MHK, Cao Y, Leung TY, Kwok YK, Choy KW, Dong Z#

Genes 2023; 14(7):1357

Investigation of the genetic etiology in male infertility with apparently balanced chromosomal structural rearrangements by genome sequencing

Chau MHK, Li Y, Dai P, Shi M, Zhu X, Chung JPW, Kwok YK, Choy KW, Kong X, Dong Z#

Asian J Androl. May-Jun 2022;24(3):248-254

Trio-Based Low-Pass Genome Sequencing Reveals Characteristics and Significance of Rare Copy Number Variants in Prenatal Diagnosis

Chau MHK, Qian J, Chen Z, Li Y, Zheng Y, Tse WT, Kwok YK, Leung TY, Dong Z,# Choy KW#

Front Genet. 2021 Sep 20;12:742325

Low-pass genome sequencing-based detection of absence of heterozygosity: validation in clinical cytogenetics

Dong Z, Chau MHK, Zhang Y, Yang Z, Shi M, Wah YMI, Kwok YK, Leung TY, Morton C, Choy KW

Genet Med. 2021 Jul;23(7):1225-1233

Deciphering the complexity of simple chromosomal insertions by genome sequencing

Dong Z, Chau MHK, Zhang Y, Dai P, Zhu X, Leung TY, Kong X, Kwok YK, Stankiewicz P, Cheung SW, Choy KW

Hum Genet. 2021 Feb;140(2):361-380

Low-pass genome sequencing: a validated method in clinical cytogenetics.

Chau MHK, Wang H, Lai Y, Zhang Y, Xu F, Tang Y, Wang Y, Chen Z, Leung TY, Chung JPW, Kwok YK, Chong SC, Choy KW, Zhu Y, Xiong L, Wei W, Dong Z#

Hum Genet. 2020 Nov;139(11):1403-1415

Low-pass genome sequencing versus chromosomal microarray analysis: implementation in prenatal diagnosis

Wang H,* Dong Z,* Zhang R,* Chau MHK,* Yang Z, Tsang K, Wong HK, Gui B, Meng Z, Xiao K, Zhu X, Wang Y, Chen S, Leung TY, Cheung SW, Kwok YK, Morton CC, Zhu Y, Choy KW

Genet Med, 2020 Mar;22(3):500-510

Genome Sequencing Explores Complexity of Chromosomal Abnormalities in Recurrent Miscarriage.

Dong Z, Yan J, Xu F, Yuan J, Jiang H, Wang H, Chen H, Zhang L, Ye L, Xu J, Shi Y, Yang Z, Cao Y, Chen L, Li Q, Zhao X, Li J, Chen A, Zhang W, Wong HG, Qin Y, Zhao H, Chen Y, Li P, Ma T, Wang WJ, Kwok YK, Jiang Y, Pursley AN, Chung JPW, Hong Y, Kristiansen K, Yang H, Piña-Aguilar RE, Leung TY, Cheung SW, Morton CC, Choy KW, Chen ZJ.

Am J Hum Genet. 2019 Dec 5;105(6):1102-1111.

Development of Coupling Controlled Polymerizations by Adapter-ligation in Mate-pair Sequencing for Detection of Various Genomic Variants in One Single Assay

Dong Z, Zhao X, Li Q, Yang Z, Xi Y, Alexeev A, Shen H, Wang O, Ruan J, Ren H, Wei H, Qi X, Li J, Zhu X, Zhang Y, Dai P, Kong X, Kirkconnell K, Alferov O, Giles S, Yamtich J, Kermani B, Dong C, Liu P, Mi Z, Zhang W, Xu X, Drmanac R, Choy KW, Jiang Y

DNA Res. 2019 Aug 1;26(4):313-325

Prenatal Diagnosis of Fetuses with Increased Nuchal Translucency by Genome Sequencing Analysis

Choy KW, Wang H, Shi M, Chen J, Yang Z, Zhang R, Yan H, Wang Y, Chen S, Chau MHK, Cao Y, Chan OYM, Kwok YKY, Zhu Y, Chen M, Leung TY, Dong Z#

Front Genet. 2019 Aug; volume 10:761 (14 pages)

Identification of balanced chromosomal rearrangements previously unknown among participants in the 1000 Genomes Project: implications for interpretation of structural variation in genomes and the future of clinical cytogenetics

Dong Z, Wang H, Chen H, Jiang H, Yuan J, Yang Z, Wang WJ, Xu F, Guo X, Cao Y, Zhu Z, Geng C, Cheung CWC, Kwok YKY, Yang H, Leung TY, Morton CC, Cheung SW, Choy KW

Genet Med. 2018 Jul;20(7):697-707

Balanced Chromosomal Rearrangement Detection by Low-Pass Whole-Genome Sequencing

Dong Z, Ye L, Yang Z, Chen H, Yuan J, Wang H, Guo X, Li Y, Wang J, Chen F, Cheung SW, Morton CC, Jiang H, Choy KW

Curr Protoc Hum Genet. 2018 Jan 24;96:8.18.1-8.18

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

Dong Z, Xie, W, Chen, H, Xu, J, Wang, H, Li, Y, Wang, J, Chen, F, Choy KW, Jiang H

Curr Protoc Hum Genet 2017 Jul 11;94:8 17 1-8 17 16

Low-pass Whole-genome Sequencing in Clinical Cytogenetics: A Validated Approach

Dong Z, Zhang J, Hu P, Chen H, Xu J, Tian Q, Meng L, Ye Y, Wang J, Zhang M, Li Y, Wang HL, Yu S, Chen F, Xie J, Jiang H, Wang W, Choy KW, Xu Z

Genet Med Sep 2016;18(9): 940 – 948

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

Dong Z, Jiang LP, Yang CC, Hu H, Wang XH, Chen HX, Choy KW, Hu HM, Dong YL, Hu B, Xu JC, Long Y, Cao SJ, Chen H, Wang WJ, Jiang H, Xu FP, Yao H, Xu X, Liang ZQ

Hum Mutat 2014;35(5): 625 – 636