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SMRT Grant Winners: Three Scientists Selected to Use HiFi Sequencing to Tackle Genomic Challenges

Wednesday, March 11, 2020

Apply for the 2019 HiFi for All SMRT Grant to discover how highly accurate long reads can advance your science

 

PacBio highly accurate long reads, known as HiFi reads, offer all the benefits of long-read sequencing with accuracy comparable to short-read sequencing. To celebrate this new paradigm in sequencing technology, we hosted the 2019 HiFi for All SMRT Grant this past fall. This SMRT Grant was open to scientists worldwide and offered three winning projects each up to six SMRT Cells 8M and sequencing on the Sequel II System by our Certified Service Providers and co-sponsors.

In response to our call for projects across the range of SMRT Sequencing applications, we received many truly compelling proposals, which made selecting the winners quite a challenge. Today, we are thrilled to announce the three winners of this SMRT Grant and share a glimpse into how they will use HiFi sequencing to tackle a diverse set of scientific questions.

 

Holding on by a Claw: Elucidating the Genomics of the African Leopard

Winner: Ellie Armstrong (@_ellie_cat), Stanford University

A young leopard poses for a photo in the Okavango Delta, Botswana. Photo by Ellie Armstrong.

Synopsis: This project will generate a high-quality genome assembly for the African leopard, a big cat facing endangered status due to habitat loss, hunting, and illegal wildlife trade. Very little genetic information has been produced for leopards. A high-quality assembly will be important for conservation genomics and for investigating genetic and structural variation across leopard subspecies.

“We are thrilled to be working with PacBio to produce a high-quality assembly of the African leopard. Leopards are extremely elusive, making them a prime species for the development of genomic monitoring tools. This genome will allow us to investigate the distribution of genomic diversity of leopards, their evolutionary history, and gain insight into how they adapt to such a wide variety of landscapes.” – Ellie Armstrong

 

Sequencing for this project will be provided by Georgia Genomics and Bioinformatics Core.

 


 

Establishing the Largest Longitudinal HIV Sequence Database Ever Assembled

Winner: Daniel Sheward (@DannySheward), University of Cape Town

The HIV Diversity and Pathogenesis Group at the Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, South Africa.

Synopsis: In a collaboration between the University of Cape Town (PI: Carolyn Williamson), the National Institute of Communicable Diseases of South Africa (PI: Penny Moore) and the Karolinska Institutet (PI: Ben Murrell), scientists will use PacBio sequencing for more than 1,000 samples collected from 150 women in the South African CAPRISA Acute Infection cohort to perform a longitudinal study of HIV infection. A highly multiplexed approach will allow for HiFi sequencing of the virus in all samples to generate the largest sequence database of longitudinally collected HIV samples. The information gleaned from this database is expected to contribute to the research community’s understanding of viral evolution, latency, immunology and vaccine development.

“We are extremely excited about this project.  With HiFi sequencing on the Sequel II System, a project of this scope is finally feasible.”  – Daniel Sheward

 

Sequencing for this project will be provided by the Earlham Institute.

 


 

Asian Reference Genome

Three ethnic groups (Chinese, Malays and Indians) of Singapore population. Image credit: Gloria Fuentes – The Visual Thinker LLP.

Winner: Jianjun Liu, Genome Institute of Singapore

Synopsis: With this SMRT Grant, scientists will sequence the genomes of three individuals — one each of Chinese, Indian, and Malay descent. This is part of a larger effort at the Genome Institute of Singapore to generate Asian population-specific reference genomes for improved variant calling for people in these populations. The assemblies produced through the SMRT Grant will be used to analyze structural variation, evaluate different genome assemblers and adapt the Institute’s methods for HiFi data. Ultimately, population-specific data will play an important role in the implementation of precision medicine for people of all ancestries.

“We are excited about this project and very thankful for support by PacBio and DNA Link. Genomic analysis of Asian populations has fallen behind the efforts in western populations. We hope that our effort can help to improve it by providing tools and resources that can empower the studies of Asian populations.”   – Jianjun Liu

 

Sequencing for this project will be provided by DNA Link, Inc.

 


Congratulations to all our HiFi for All SMRT Grant winners! And thank you to our co-sponsors for teaming up with PacBio to make these SMRT Grants possible. Explore the 2020 SMRT Grant Programs to apply to have your project funded.

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