Singapore Launches Long-Read Population Sequencing Program with PacBio, Oxford Nanopore

By Bio-IT World Staff

August 8, 2024 | Singapore’s National Precision Medicine (NPM) program has launched a long-read sequencing project to gain deeper insights into Asian genetic diversity. The program, Precision Health Research, Singapore (PRECISE) has appointed both Oxford Nanopore Technologies (ONT) and PacBio (PacBio) to deliver sequencing.

The goals of the project are to deliver a reference genome for the Asian population, build a structural variant catalogue representing multi-ethnic Singapore, and facilitate advancements in the clinical diagnoses of rare genetic diseases and pediatric cancers.

This long-read sequencing project is part of Phase II of Singapore’s NPM program, led by PRECISE and jointly supported by research partners Lee Kong Chian School of Medicine, Genome Institute of Singapore (GIS), A*STAR - Agency for Science, Technology and Research, KK Women's and Children's Hospital, and the National Cancer Centre Singapore (NCCS).

Both ONT and PacBio will be engaging local service providers, NovogeneAIT Genomics and Macrogen Inc. SG, to advance capacity building and knowledge transfer. This development will not only enhance Singapore’s technical capabilities in this sector, but also create upskilling and employment opportunities for professionals here who are in the field of genomics technologies.

Oxford Nanopore’s PromethION 48

Oxford Nanopore’s portion of the project will focus on sequencing 10,000 genomes representing Singapore’s diverse population, including Malay, Indian, and Chinese communities participating in the PRECISE-SG100K population cohort. This project will use Oxford Nanopore’s fleet of high-output PromethION 48 sequencing devices to deliver detailed, comprehensive genomic data to advance research and support precision healthcare.

Oxford Nanopore has made strategic investments in Singapore, which it has positioned as a commercial hub for the Asia Pacific region. The company recently expanded its laboratory facilities in Singapore to support increased activities in training, knowledge transfer, and the up-skilling of local technical staff. This includes deploying sequencers within the Science Centre Singapore and the Singapore Institute of Technology for use within high school, undergraduate and adult education programs. Additionally, the company has access to a distribution facility in Singapore through its expanded partnership with UPS Healthcare, resulting in faster delivery of flow cells to Singapore and across the Asia Pacific.

“We are excited to collaborate with Singapore’s National Precision Medicine (NPM) programme to create one of the most extensive and inclusive reference genome datasets globally,” said Gordon Sanghera, CEO of Oxford Nanopore, in a press release. “This collaboration not only enhances our commitment to precision healthcare but also strategically positions Singapore as a pivotal hub for genomics in the Asia Pacific, fostering significant advancements in medical research and healthcare outcomes.”

Other partners in this project, including NovogeneAIT, demonstrate a strong collaborative effort to leverage innovative technology in genomics, Oxford Nanopore noted.

Revio HiFi

PRECISE has also chosen Pacific Bioscience’s Revio HiFi sequencing system as part of the program. PacBio’s long-read sequencing provides comprehensive genomic coverage, enabling the detection of large structural variations and DNA methylation, providing a more complete picture of the genome. This multi-omics approach combines whole genome sequencing (WGS), RNA full-length sequencing, fiber sequencing, and methylation analysis.

“I am delighted that PRECISE has selected our Revio system for their extensive, flagship long-read sequencing project in Singapore,” said Christian Henry, President and Chief Executive Officer of PacBio in a press release. “PRECISE chose PacBio HiFi technology for its capacity to deliver complete and accurate genomes. This project exemplifies Revio’s unique ability to provide differentiated solutions for large-scale, multi-thousand-sample, whole genome sequencing projects.”

PacBio will generate high-quality phased methylome and genomic information for a multi-thousand-sample whole genomes sequencing project, including 60x HiFi depth for Pan-Asian reference genomes; 20x HiFi depth for multi-omics analysis; and 30x HiFi depth for unresolved and research cases in cancer and rare diseases.

PacBio plans to establish advanced sequencing and data analysis pipelines in Singapore, including a centralized library preparation facility and sequencing laboratory for high throughput production. Macrogen Asia Pacific Pte Ltd, the first CAP-accredited service provider in Singapore for Whole Genome Sequencing (WGS), will execute the PacBio long-read sequencing production. PacBio will use AWS cloud storage and workflow capabilities to ensure secure and efficient data processing and delivery for PRECISE researchers and clinicians.