The Chinese University of Hong Kong & Prince of Wales Hospital

Department of Obstetrics and Gynaecology
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Dr. Dong Zi Rui, Elvis

Dr. Dong Zi Rui, Elvis Assistant Professor
(852) 3505 3099 elvisdong@cuhk.edu.hk

Biography

Dr. DONG, Zirui Elvis is an Assistant Professor and an Assistant Director (Bioinformatics) of the Prenatal Diagnostic Laboratory in the Department of Obstetrics and Gynaecology at the Chinese University of Hong Kong, an Honorary Scientific Officer (Medical), in Prince of Wales Hospital, Hospital Authority, and an Honorary Researcher in the Great Ormond Street Hospital for Children, United Kingdom. He also acts as a committee member in several societies including the Reproductive Genetics Branch of the Genetics Society of China.

He has made significant strides in human genomics, particularly through developing bioinformatic algorithms and analytical pipelines, which are pivotal for genomic structural variants diagnosis and research in fetal medicine, and male and female infertility. He and the team have also demonstrated a high prevalence of rare structural variants underlying the pathogenicity of different disease development through multi-omic investigations. His work has gained widespread recognition internationally and the genomic assays have been adopted by the Hospital Authority in Hong Kong for both clinical and research application. The analytical pipelines for genomic investigations have also been filed patents, two of which have been granted by China and Singapore. To facilitate understanding of the tissue/cell-type/timepoint specific gene expression profiling and to assist gene discovery, his team also established a Temporal Expression during Development Database (TEDD), v2.0 of which integrates over 15.9 million cells from 9 species, and is empowered with three in-silico analytical modules with cloud-based job submission interface.

He has published over 50 articles, over 20 of which he served as the first/corresponding author, featured in prestigious journals including American Journal of Human Genetics, Nucleic Acids Research, and Clinical Chemistry. He has also presented the study findings in over 30 international conferences as platform or invited presentations including five times in the annual meeting of the American Society of Human Genetics (ASHG). He serves as the Principal Investigator of 12 external competitive grants (GRF, NSFC, HMRF, and ITF), and as a Co-I in a CRF and a National Key R&D program. He received multiple awards including the Young Investigator Award from ASPIRE (Asia Pacific Initiative on Reproduction) and two Gold Medals at the International Invention Fairs. Currently, he serves as an Associate Editor for Science China-Life Sciences and BMC Genomics.

Education

PhD in Genetics, Department of Obstetrics and Gynacology, The Chinese University of Hong Kong

Research Interest(s)

  • Development and implementation of detection algorithms and analytical pipelines based on short-read and long-read Genome Sequencing (GS) for unbiasedly identifying clinically significant copy-number variants (CNVs), genomic structural variants (SVs, e.g., balanced translocations, inversions and insertions) and regions with absence of heterozygosity (AOHs, e.g., uniparental disomy and parental consanguinity) in prenatal, paediatric and adult congenital diseases as well as cancers (paediatric leukemia);
  • Deciphering the spectrums and profiles of genomic structural variants through large scale cohort study, and establishment of the curation and interpretation database for genomic SV (cidSV online database) to understand the differences of SV spectrum between patients with variable diseases and presumably healthy subjects.
  • Investigation on SV’s impact to human diseases (fetal ultrasound anomalies, and human male and female infertility) through a multi-omics approach including alternation in 3D organization (with Hi-C), chromatin interaction (4C-seq) and cell-type/organ/timepoint-specific gene expression aberration (bulk and single-cell RNA-seq, histone modification (ChIP-seq) and chromatin accessibility (ATAC-seq) with functional validations by cellular and mouse models;
  • Study on the potential formation mechanism of genomic structural variants (e.g., chromosomal insertion and chromothripsis) by establishing induced DNA damage cellular models and analysis with in-house single-cell mate-pair sequencing.
  • Development and establishment of Temporal Expression during Development Database (TEDD online database) by curation, reanalysis and integration of single-cell RNA and ATAC-seq based datasets derived from multi-developmental timepoints from human and different model organisms, and by enabling cloud-based analytical platforms to facilitate understanding of cell-type, tissue-, organ- and timepoint specific gene expression and regulation networks.  

Specialisations

  • Clinical Bioinformaticis
  • Genomic medicine
  • Genetics

Qualifications

  • BSc (SCUT), MSc (CUHK), PhD (CUHK)

Awards and Honours

  • Young Investigator Award. The Asia Pacific Initiative on Reproduction (ASPIRE). The 15th Congress of the Asia Pacific Initiative on Reproduction (ASPIRE 2026), 05/2026
  • Gold Medal for the invention: Methods For Detecting Absence of Heterozygosity By Low-Pass Genome Sequencing, showcased at the fair held on Dec 4-5,2025. The 5th Asia Exhibition of Innovations and Inventions Hong Kong, Hong Kong.
  • Gold Medal with Congratulations of the Jury in recognition of excellent to invent: Methods For Detecting Absence of Heterozygosity By Low-Pass Genome Sequencing, showcased at the fair held on Feb 16-19, 2025. The 15th International Invention Fair in the Middle East, Kuwait.

Others

  • 2025-present: Committee Member, The Reproductive Genetics Branch of the Genetics Society of China
  • 2025-present: Member, The British Society for Genetic Medicine (BSGM), United Kingdom
  • 2023-present: Standing Committee Member, Professional Committee on Reproductive and Genetic Management, Association for Medical Education of Guangdong Province, China
  • 2021-present: Member, Fertility Preservation Research Centre, CUHK
  • 2021-present: Associate member, Hong Kong Hub of Obstetrics and Paediatric Excellence, CUHK Research Institute at Hong Kong Children’s Hospital, CUHK.
  • 2020-present: Standing Committee Member, Clinical Genetics and Genetic Counseling Board (CGGCB), Shanghai Society of Genetics, China, since
  • 05/2020-present: Member, Chinese Board of Genetic Counseling, China
  • 2019-present: 副研究员, 香港中文大学深圳研究院, 深圳
  • 2017-present: Life-time Member: Association of Chinese Geneticists in America (ACGA), United States of America
  • 2016-present: Member, American Society of Human Genetics

Patent

  • Methods for detecting absence of heterozygosity by low-pass genome sequencing. Granted by China (ZL 2020 8 0058883.5) and Singapore (11202201848Q)
  • Methods to Determine Maternity, Paternity, or Parentage and Computer Systems for Implementation. Filed: U.S. Non-provisional Patent Application No. 18/672,159; International Patent Application No. PCT/CN2024/096268

Business Leadership

  • 2021-2022: Core team member, Laboratory Genetics and Genomics supported by the “MAKE a DASH” program of Hong Kong SAR government (600,000 HKD) and received an award as “The Best Team”

Researcher ID

Grants

He serves as a PI of 12 external competitive grants including GRF (#14117524), RGC Germany/Hong Kong Joint Research Scheme (#G-CUHK404/25), HMRF (#07186576, 8190226, 09200236 and 12230606), ITF (#PRP/042/22FX), NSFC (#31801042 and 32270678) and NSFGD (#2023A1515030220). In addition, he also serves as a Co-PI of a CRF (#C4062-21GF) and of a National Key R&D Program of China (#2025YFC2708200).

Postgraduate Students

Former students: Yanyan ZHANG (PhD); Jicheng QIAN (PhD); Ziheng ZHOU (PhD)
Current students:
As a supervisor: Lin CHEN (PhD); Jingwen HU (PhD); Mingyang YU (PhD); King Kin LAM (PhD); Simin LIU (PhD)
As a co-supervisor: Jia ZHENG (PhD); Keying LI (PhD)

Editorships

1
Prenatal Tympanic Ring Anomaly Without Microtia: A Subtle Clue Toward Severe Early-Onset Monogenic Disorders Lam YH, Shi M, Dong Z, Choy KW, Leung TY, Cao Y Prenatal Diagnosis, 2026 Jun;46(7):1096-1103
2
Prenatal-Onset Recessive Titinopathies: Clinical Spectrum, Genotype–Phenotype Correlations, and Outcomes Zheng Y, Shi M, Zhao Y, Chung TCY, Chau MHK, Dong Z, Kwok YKY, Kwan HWA, Chong JSC, Leung TY, Lo TK, Choy KW, Zhang Y, Cao Y* Diagnostics, 2026 Jun;16(11):1723
3
NONO-Related Syndromic X-Linked Developmental Disability 34: Further Clinical and Molecular Delineation in a Prenatal Cohort Zhao Y, Zou G, Shi M, Law KM, Lau SL, Meng M, Ting YH, Poon CYL, Dong Z, Chau MHK, Leung TY, Choy KW, Zhang X, Cao Y Prenatal Diagnosis, 2026 May; 46(5-6):914-923
4
TEDD 20: an advanced temporal gene expression database enabled by in-silico functional analyses for developmental mechanism investigation Chan CC, Lam KK, Chen L, Yu M, Hu J, Zhu Y, Zheng Y, Zheng J, Choy KW, Dong Z* SCIENCE CHINA Life Sciences, Mar 2026;69(3):993-1007
5
Identification of pathogenic genomic variants in idiopathic azoospermia by long-fragment-read genome sequencing: abridged secondary publication Dong Z, Leung TY, Chung JPW, Cao Y Hong Kong Medical Journal, 2026 Feb;32(1 Supplement 1):17-21
6
Clinical validation of artificial intelligence-assisted karyotyping on peripheral blood in a cytogenetic diagnostic laboratory Zhu Y, Chau MHK, Wang H, Song N, Wei R, Suen KW, Chan CSA, Hung WC, Cao Y, Dong Z, Leung TY, Cheung SW, Choy KW Human Genetics, 2025 Dec; 144(11-12):1269-1276
7
Mate-pair low-pass genome sequencing for prenatal diagnosis of fetuses with ultrasound anomalies: abridged secondary publication Dong Z*, Leung T Y, Lo IFM, Kwok YKY Hong Kong medical journal, Oct 2025;31(Suppl 7):S13-17
8
Book Title: Genomic Detection and Delineation of Chromoanasynthesis by Mate-Pair Sequencin
Chapter Title: Chromoanagenesis : Methods and Protocols Zheng Y, Zhang Y, Cheung SW, Choy KW, Dong Z, Gu S Humana Press, 2025 Aug;2968:111-129
9
3D visualization of uterus and ovary: tissue clearing techniques and biomedical applications Liu Q, Song Z, Liu S, Dong Z, Zheng X, Leung TY, Chen X Frontiers in Bioengineering and Biotechnology, 2025 Jul;13:1610539
10
Mate-pair Sequencing Enables Identification and Delineation of Balanced and Unbalanced Structural Variants in Prenatal Cytogenomic Diagnostics Qian J, Wang H, Liang H, Zheng Y, Yu M, Tse WT, Kwan AHW, Wong L, Wong NKL, Wah IYM, Lau SL, Hui ASY, Chau MHK, Chen X, Zhang R, Poon L C, Leung TY, Liu P, Choy KW, Dong Z Clin Chem. 2025 Jan 3;71(1):155-168
11
Detection of genomic variants by genome sequencing in foetuses with central nervous system abnormalities Wang Y, Liu M, Gao Z, Hua C, Jiang J, Zheng Y, Dong Z, Cao Y, Choy KW, Zhu X, Kong X Ann Med. 2024 Dec;56(1):2399317
12
Contribution of Genomic Imbalance in Prenatal Congenital Anomalies of the Kidney and Urinary Tract: A Multi-Center Cohort Study Li K, Wang H, Chau MHK, Dong Z, Cao Y, Zheng Y, Leung TY, Choy KW, Zhu Y Prenat Diagn. 2024 Nov;44(12):1451-1461
13
Genome sequencing in the prenatal diagnosis of structural malformations in the fetus Chau MHK, Choolani M, Dong Z, Cao Y, Choy KW Best Pract Res Clin Obstet Gynaecol. 2024 Sep 13:102539
14
Identification of cryptic balanced translocations in couples with unexplained recurrent pregnancy loss based upon embryonic PGT-A results Li S, Li H, Gao Y, Zou Y, Yin X, Chen ZJ, Choy KW, Dong Z, Yan J Journal of Assist Reprod Genet. 2024 Jan;41(1):171- 184
15
Incremental yield of whole genome sequencing over chromosome microarray and exome sequencing for congenital anomalies in prenatal period and infancy: systematic review and meta-analysis Shreeve N, Sproule C, Choy KW, Dong Z, Gajewska-Knapik K, Kilby MD, Mone F Ultrasound Obstet Gynecol. 2024 Jan;63(1):15-23
16
Prenatal diagnosis of polycystic kidney caused by biallelic hypomorphic variants in the PKD1 gene Zheng Y, Wong L, Kwan AHW, Dong Z, Kwok KY, Choy KW, Dai H, Cao Y Prenat Diagn. 2024 Feb;44(2):247-250
17
Single-cell analysis reveals specific neuronal transition during mouse corticogenesis Zhou Z., Pan Y., Zhou S., Wang S., Zhang D., Cao Y., Jiang X., Li J., Zhu L., Zhao L., Gu S., Lin G., Dong Z., Sun H.X. Front Cell Dev Biol. 2023 Nov 6:11:1209320
18
A Pilot Investigation of Low-pass Genome Sequencing Identifying Site-Specific Variation in Chromosomal Mosaicisms by a Multiple Site Sampling Approach in First-trimester Miscarriages Li Y, Chau MHK, Zhang YX, Zhao YL, Xue SW, Li TC, Cao Y, Dong Z, Choy KW, Chung JPW Hum Reprod. 2023 Aug 1;38(8):1628-1642
19
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 Jul; 14(7):1357
20
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
21
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
22
Molecular cytogenomics of human genetic disorders Dong Z, Choy KW, Morton CC In: Human Reproductive and Prenatal Genetics (Second Edition), Academic Press. 2023, Chapter 28, pp 721-741
23
Editorial: Chromosome structural variants: Epidemiology, identification and contribution to human diseases Dong Z, David D, Gonzaga-Jauregui C, Morton CC, Zepeda-Mendoza CJ Front Genet. 2022 Sep 9;13:1022918
24
Exploring the diagnostic utility of genome sequencing for fetal congenital heart defects Cao Y, Chau MHK, Zheng Y, Zhao Y, Kwan AHW, Hui SYA, Lam YH, Tan TYT, Tse WT, Wong L, Leung TY, Dong Z, Choy KW Prenat Diagn. 2022 Jun;42(7):862-872. (Impact factor (2022): 3.0, citations: 6
25
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
26
The Burden and Benefits of Knowledge: Ethical Considerations Surrounding Population-Based Newborn Genome Screening for Hearing Mitchell CO, Rivera-Cruz G, Chau MHK, Dong Z, Choy KW, Shen J, Amr S, Giersch ABS, Morton CC Int J Neonatal Screen. 2022 May 27;8(2):36
27
Investigation of chromosomal structural abnormalities in patients with undiagnosed neurodevelopmental disorders Cao Y, Luk HM, Zhang YY, Chau MHK, Xue S, Cheng SSW, Li AM, Chong JSC, Leung TY, Dong Z, Choy KW, Lo IFM Front Genet. 2022 Apr 14;13:803088
28
SVInterpreter: A Comprehensive Topologically Associated Domain-Based Clinical Outcome Prediction Tool for Balanced and Unbalanced Structural Variants Fino J, Marques B, Dong Z, David D Front Genet. 2021 Dec 1;12:757170
29
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
30
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
31
Performance of Cell-Free DNA Screening for Fetal Common Aneuploidies and Sex Chromosomal Abnormalities: A Prospective Study from a Less Developed Autonomous Region in Mainland China Lai Y, Zhu X, He S, Dong Z, Tang Y, Xu F, Chen Y, Meng L, Tao Y, Yi S, Su J, Huang H, Luo J, Leung TY, Wei H Genes 2021 Mar;12(4):12040478
32
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
33
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
34
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
35
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.
36
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
37
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)
38
Chronic inflammatory lesions of the placenta are associated with an up-regulation of amniotic fluid CXCR3: A marker of allograft rejection Maymon E, Romero R, Bhatti G, Chaemsaithong P, Gomez-Lopez N, Panaitescu B, Chaiyasit N, Pacora P, Dong Z, Hassan SS, Erez O J Perinat Med. 2018 Feb 23;46(2):123-137
39
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
40
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
41
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
42
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
43
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