The implementation of genome sequencing in rare genetic diseases diagnosis: a pilot study from the Hong Kong genome projectResearch in context
Summary: Background: Genome sequencing (GS) has revolutionised the diagnostic odyssey of patients with rare genetic diseases (RDs) and accelerated large-scale genome projects globally. However, the impact of GS on patients with RDs is yet to be investigated among genome projects in Asia. The Hong K...
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2025-02-01
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| Series: | The Lancet Regional Health. Western Pacific |
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| author | Wai Kei Jacky Lam Chak Sing Lau Ho Ming Luk Lisa Wing Chi Au Gary C.P. Chan Will Yap Hang Chan Shirley Sze Wing Cheng Timothy Hua Tse Cheng Li Li Cheung Yiu Fai Cheung Josephine Shuk Ching Chong Annie Tsz Wai Chu Claudia Ching Yan Chung Kin Lai Chung Cheuk Wing Fung Eva Lai Wah Fung Yuan Gao Stephanie Ho Shirley Pik Ying Hue Chi-Ho Lee Tsz Leung Lee Philip Hei Li Hei Man Lo Ivan Fai Man Lo Herbert Ho Fung Loong Becky Mingyao Ma Wei Ma Shirley Yin Yu Pang Wai-Kay Seto Steven Wai Kwan Siu Ho So Yuk Him Tam Wenshu Tang Rosanna Ming Sum Wong Desmond Yat Hin Yap Maggie Lo Yee Yau Brian Hon Yin Chung Su-Vui Lo |
| author_facet | Wai Kei Jacky Lam Chak Sing Lau Ho Ming Luk Lisa Wing Chi Au Gary C.P. Chan Will Yap Hang Chan Shirley Sze Wing Cheng Timothy Hua Tse Cheng Li Li Cheung Yiu Fai Cheung Josephine Shuk Ching Chong Annie Tsz Wai Chu Claudia Ching Yan Chung Kin Lai Chung Cheuk Wing Fung Eva Lai Wah Fung Yuan Gao Stephanie Ho Shirley Pik Ying Hue Chi-Ho Lee Tsz Leung Lee Philip Hei Li Hei Man Lo Ivan Fai Man Lo Herbert Ho Fung Loong Becky Mingyao Ma Wei Ma Shirley Yin Yu Pang Wai-Kay Seto Steven Wai Kwan Siu Ho So Yuk Him Tam Wenshu Tang Rosanna Ming Sum Wong Desmond Yat Hin Yap Maggie Lo Yee Yau Brian Hon Yin Chung Su-Vui Lo |
| author_sort | Wai Kei Jacky Lam |
| collection | DOAJ |
| description | Summary: Background: Genome sequencing (GS) has revolutionised the diagnostic odyssey of patients with rare genetic diseases (RDs) and accelerated large-scale genome projects globally. However, the impact of GS on patients with RDs is yet to be investigated among genome projects in Asia. The Hong Kong Genome Project (HKGP) was implemented to benefit patients and families with RDs in Hong Kong, and to increase the inclusiveness of Chinese genomic data. This study evaluated the impact of short read GS (srGS), complemented by long read GS (lrGS) in a subset, on individuals recruited in the pilot phase of the HKGP. Methods: GS was performed on a prospective cohort of patients with suspected genetic disease recruited by territory-wide referrals to the HKGP. All participants received srGS, while lrGS was applied to a subset to resolve technically challenging regions unclear from srGS and provide phasing information for potential compound heterozygous variants. A phenotypic-driven diagnostic workflow was implemented to filter and prioritise rare and likely disease-causing variants. The primary outcome was diagnostic yield. The impact on the diagnostic odyssey and clinical management was also assessed. Findings: A total of 1264 individuals from 520 families with a broad spectrum of RDs were recruited, with 94% of probands being Chinese. srGS was performed for all individuals and lrGS was performed in 21 individuals. The use of srGS achieved a molecular diagnosis in 24% (125/520) of probands, and an additional 4% (21/520) with the assistance from lrGS. Approximately one-third of the identified diagnostic variants being novel. Diagnostic yield was found to be significantly higher among adult probands compared to paediatric probands (32% vs 24%; p = 0.025). The diagnostic yield was significantly higher in probands without prior genetic testing (37%; n = 185) compared to those previously tested, including exome and genome sequencing (23%; n = 335) (p = 0.001). GS ended diagnostic odysseys with an average length of 15 years (0.5–59), and potentially impacted clinical management in 77% (113/146) of diagnosed probands. Interpretation: This population-based genome project shed light on the consideration of integrating srGS and lrGS in clinical workflows for RDs. The identification of unique and prevalent variants from Southeast Asia increased the inclusiveness of Chinese genomic data, contributing to greater representation and genomic diversity. Funding: The HKGP is a publicly funded genome sequencing initiative commissioned by the Health Bureau of the HKSAR Government. |
| format | Article |
| id | doaj-art-4b17af3f65cd4a0798c80ede756b3c12 |
| institution | Kabale University |
| issn | 2666-6065 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | The Lancet Regional Health. Western Pacific |
| spelling | doaj-art-4b17af3f65cd4a0798c80ede756b3c122025-01-30T05:15:02ZengElsevierThe Lancet Regional Health. Western Pacific2666-60652025-02-0155101473The implementation of genome sequencing in rare genetic diseases diagnosis: a pilot study from the Hong Kong genome projectResearch in contextWai Kei Jacky Lam0Chak Sing Lau1Ho Ming Luk2Lisa Wing Chi Au3Gary C.P. Chan4Will Yap Hang Chan5Shirley Sze Wing Cheng6Timothy Hua Tse Cheng7Li Li Cheung8Yiu Fai Cheung9Josephine Shuk Ching Chong10Annie Tsz Wai Chu11Claudia Ching Yan Chung12Kin Lai Chung13Cheuk Wing Fung14Eva Lai Wah Fung15Yuan Gao16Stephanie Ho17Shirley Pik Ying Hue18Chi-Ho Lee19Tsz Leung Lee20Philip Hei Li21Hei Man Lo22Ivan Fai Man Lo23Herbert Ho Fung Loong24Becky Mingyao Ma25Wei Ma26Shirley Yin Yu Pang27Wai-Kay Seto28Steven Wai Kwan Siu29Ho So30Yuk Him Tam31Wenshu Tang32Rosanna Ming Sum Wong33Desmond Yat Hin Yap34Maggie Lo Yee Yau35Brian Hon Yin Chung36Su-Vui Lo37Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong Special Administrative Region, China; Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, ChinaDepartment of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, ChinaDepartment of Clinical Genetics, Hong Kong Children's Hospital, Hong Kong Special Administrative Region, ChinaDepartment of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong Special Administrative Region, ChinaDepartment of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong Special Administrative Region, ChinaDivision of Cardiology, Department of Medicine, Queen Mary Hospital, Hong Kong Special Administrative Region, China; School of Clinical Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, ChinaDepartment of Clinical Genetics, Hong Kong Children's Hospital, Hong Kong Special Administrative Region, ChinaDepartment of Pathology, Hong Kong Children's Hospital, Hong Kong Special Administrative Region, ChinaDepartment of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong Special Administrative Region, ChinaDepartment of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong Special Administrative Region, China; Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, ChinaDepartment of Paediatrics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong Special Administrative Region, ChinaHong Kong Genome Institute, Hong Kong Special Administrative Region, ChinaHong Kong Genome Institute, Hong Kong Special Administrative Region, ChinaPrince of Wales Hospital, Hong Kong Special Administrative Region, ChinaDepartment of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong Special Administrative Region, ChinaDepartment of Paediatrics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong Special Administrative Region, China; Department of Paediatrics, Prince of Wales Hospital, Hong Kong Special Administrative Region, ChinaDivision of Neurology, Department of Medicine, Queen Mary Hospital, School of Clinical Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, ChinaDepartment of Clinical Genetics, Hong Kong Children's Hospital, Hong Kong Special Administrative Region, ChinaHong Kong Genome Institute, Hong Kong Special Administrative Region, ChinaDepartment of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, ChinaHospital Chief Executive Office, Hong Kong Children's Hospital, Hong Kong Special Administrative Region, ChinaDivision of Rheumatology and Clinical Immunology, Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, ChinaHong Kong Genome Institute, Hong Kong Special Administrative Region, ChinaDepartment of Clinical Genetics, Hong Kong Children's Hospital, Hong Kong Special Administrative Region, ChinaDepartment of Clinical Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong Special Administrative Region, China; State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, ChinaDivision of Nephrology, Department of Medicine, Queen Mary Hospital, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, ChinaHong Kong Genome Institute, Hong Kong Special Administrative Region, ChinaDivision of Neurology, Department of Medicine, Queen Mary Hospital, School of Clinical Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, ChinaDepartment of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, ChinaDepartment of Clinical Oncology, Queen Mary Hospital, Hong Kong Special Administrative Region, ChinaDepartment of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong Special Administrative Region, ChinaDepartment of Paediatric Surgery, Hong Kong Children's Hospital, Hong Kong Special Administrative Region, ChinaHong Kong Genome Institute, Hong Kong Special Administrative Region, ChinaDepartment of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong Special Administrative Region, ChinaDivision of Nephrology, Department of Medicine, Queen Mary Hospital, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, ChinaDepartment of Paediatrics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong Special Administrative Region, China; Department of Paediatrics, Prince of Wales Hospital, Hong Kong Special Administrative Region, ChinaDepartment of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Hong Kong Genome Institute, Hong Kong Special Administrative Region, China; Corresponding author. Hong Kong Genome Institute, 2/F, Building 20E, Hong Kong Science Park, Shatin, Hong Kong Special Administrative Region, China.Hong Kong Genome Institute, Hong Kong Special Administrative Region, China; Corresponding author. Hong Kong Genome Institute, 2/F, Building 20E, Hong Kong Science Park, Shatin, Hong Kong Special Administrative Region, China.Summary: Background: Genome sequencing (GS) has revolutionised the diagnostic odyssey of patients with rare genetic diseases (RDs) and accelerated large-scale genome projects globally. However, the impact of GS on patients with RDs is yet to be investigated among genome projects in Asia. The Hong Kong Genome Project (HKGP) was implemented to benefit patients and families with RDs in Hong Kong, and to increase the inclusiveness of Chinese genomic data. This study evaluated the impact of short read GS (srGS), complemented by long read GS (lrGS) in a subset, on individuals recruited in the pilot phase of the HKGP. Methods: GS was performed on a prospective cohort of patients with suspected genetic disease recruited by territory-wide referrals to the HKGP. All participants received srGS, while lrGS was applied to a subset to resolve technically challenging regions unclear from srGS and provide phasing information for potential compound heterozygous variants. A phenotypic-driven diagnostic workflow was implemented to filter and prioritise rare and likely disease-causing variants. The primary outcome was diagnostic yield. The impact on the diagnostic odyssey and clinical management was also assessed. Findings: A total of 1264 individuals from 520 families with a broad spectrum of RDs were recruited, with 94% of probands being Chinese. srGS was performed for all individuals and lrGS was performed in 21 individuals. The use of srGS achieved a molecular diagnosis in 24% (125/520) of probands, and an additional 4% (21/520) with the assistance from lrGS. Approximately one-third of the identified diagnostic variants being novel. Diagnostic yield was found to be significantly higher among adult probands compared to paediatric probands (32% vs 24%; p = 0.025). The diagnostic yield was significantly higher in probands without prior genetic testing (37%; n = 185) compared to those previously tested, including exome and genome sequencing (23%; n = 335) (p = 0.001). GS ended diagnostic odysseys with an average length of 15 years (0.5–59), and potentially impacted clinical management in 77% (113/146) of diagnosed probands. Interpretation: This population-based genome project shed light on the consideration of integrating srGS and lrGS in clinical workflows for RDs. The identification of unique and prevalent variants from Southeast Asia increased the inclusiveness of Chinese genomic data, contributing to greater representation and genomic diversity. Funding: The HKGP is a publicly funded genome sequencing initiative commissioned by the Health Bureau of the HKSAR Government.http://www.sciencedirect.com/science/article/pii/S2666606525000100Genome sequencingShort read genome sequencingLong read genome sequencingHong Kong genome projectPopulation-based genome projectRare disease |
| spellingShingle | Wai Kei Jacky Lam Chak Sing Lau Ho Ming Luk Lisa Wing Chi Au Gary C.P. Chan Will Yap Hang Chan Shirley Sze Wing Cheng Timothy Hua Tse Cheng Li Li Cheung Yiu Fai Cheung Josephine Shuk Ching Chong Annie Tsz Wai Chu Claudia Ching Yan Chung Kin Lai Chung Cheuk Wing Fung Eva Lai Wah Fung Yuan Gao Stephanie Ho Shirley Pik Ying Hue Chi-Ho Lee Tsz Leung Lee Philip Hei Li Hei Man Lo Ivan Fai Man Lo Herbert Ho Fung Loong Becky Mingyao Ma Wei Ma Shirley Yin Yu Pang Wai-Kay Seto Steven Wai Kwan Siu Ho So Yuk Him Tam Wenshu Tang Rosanna Ming Sum Wong Desmond Yat Hin Yap Maggie Lo Yee Yau Brian Hon Yin Chung Su-Vui Lo The implementation of genome sequencing in rare genetic diseases diagnosis: a pilot study from the Hong Kong genome projectResearch in context The Lancet Regional Health. Western Pacific Genome sequencing Short read genome sequencing Long read genome sequencing Hong Kong genome project Population-based genome project Rare disease |
| title | The implementation of genome sequencing in rare genetic diseases diagnosis: a pilot study from the Hong Kong genome projectResearch in context |
| title_full | The implementation of genome sequencing in rare genetic diseases diagnosis: a pilot study from the Hong Kong genome projectResearch in context |
| title_fullStr | The implementation of genome sequencing in rare genetic diseases diagnosis: a pilot study from the Hong Kong genome projectResearch in context |
| title_full_unstemmed | The implementation of genome sequencing in rare genetic diseases diagnosis: a pilot study from the Hong Kong genome projectResearch in context |
| title_short | The implementation of genome sequencing in rare genetic diseases diagnosis: a pilot study from the Hong Kong genome projectResearch in context |
| title_sort | implementation of genome sequencing in rare genetic diseases diagnosis a pilot study from the hong kong genome projectresearch in context |
| topic | Genome sequencing Short read genome sequencing Long read genome sequencing Hong Kong genome project Population-based genome project Rare disease |
| url | http://www.sciencedirect.com/science/article/pii/S2666606525000100 |
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