Research

Phen-Gen

Rare disease diagnosis

Each individual genome harbors many rare genetic variations. For families with rare genetic disorders, how does one differentiate the disease causal mutation from a host of potential candidate variants? There is a wealth of disease relevant information hidden in plain sight in public databases. We combine patient clinical information, their omics data along with this information in our prediction model. A particular focus is on unresolved difficult-to-diagnose cases where the traditional methods have failed to define a conclusive diagnosis.

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Understanding blood cancer progression

Some cancer patients survive decades post diagnosis while others live only days or months. Understanding the genetic, clinical and phenotypic variability amongst the patients and its consequence will help design personalized therapies for current and future cases. Our current focus is leukemia where we are particularly interested in studying the shifts in evolutionary trajectories and its impact on patient prognosis. The aim is to get ahead of the cancer to ward off the available routes to relapse. For this we rely on multi omics bulk and single cell technologies.

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Other cool stuff

Beyond the two main directions, we are also aiming to stretch our boundaries in various projects in immunology, and technology development. Come talk to us if you want to learn more!

Team

Xingliang

Xingliang Liu

Phd student
Research focus: leukemia, single cell analytics

Yanmin

Yanmin Zhang

Phd student
Research focus: rare neuromuscular diseases, stem cell reprogramming

Xu Ling

Xu Ling

Phd student
Research focus: rare disease analytics, statistical genomics

Yibing

Yibing Liu

MPhil student
Research focus: deep learning, breast cancer prognostication

Nicole

Nicole Saw

Research Assistant
Research focus: leukemia, precision medicine

Alexandre

Alexandre Mondaini

Research Assistant
Research focus: high performance computing, workflow design

Stanley

Chun Ming Wu Stanley

Research Assistant
Research focus: stem cell reprogramming, translational medicine

Ann

Pan Yan Anne

Research Assistant
Research focus: single cell experiments and analytics

Representative Publications

A more complete publication list

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Experimental and Bioinformatics considerations in cancer application of single cell genomics

Computational and Structural Biotechnology Journal, December 2020

Joanna Hui Juan Tan , Say Li Kong , Joyce A Tai, Huay Mei Poh, Fei Yao, Yee Yen Sia, Edwin Kok Hao Lim, Angela Maria Takano Pena, Daniel Shao-Weng Tan, Asif Javed , Axel M Hillmer

publication software

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Redefining prognostication of de novo cytogenetically normal acute myeloid leukemia in young adults

Blood Cancer Journal, October 2020

Sze P Tsui, Ho W Ip, Nicole Y Saw, Chunxiao Zhang, Arthur K Cheung, Nelson K Ng, Cheuk H Man, Stephen S Lam, Wing F Tang, Chi H Lin, Grace H Cheng, Chun H Au, Edmond S Ma, Tsun L Chan, Jason C So, Margaret H Ng, Kelvin C Cheng, Kit F Wong, Lai P Siu, Sze F Yip, Shek Y Lin, June S Lau, Tsan H Luk, Harold K Lee, Chi K Lau, Bonnie Kho, Joycelyn P Sim, Yok L Kwong, Suet Y Leung, Asif Javed , Anskar Y Leung

publication editorial comment

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An integrative model of pathway convergence in genetically heterogeneous blast crisis chronic myeloid leukemia

Blood, March 2020

Tun Kiat Ko , Asif Javed , Kian Leong Lee , Thushangi N Pathiraja , Xingliang Liu, Simeen Malik, Sheila Xinxuan Soh, Xiu Ting Heng, Naoto Takahashi, Joanna HJ Tan, Ravi Bhatia, Alexis J Khng, Wee J Chng, Yee Yen Sia, David A Fruman, King Pan Ng, Zhu En Chan, Kim JiaJing Xie, Qiangze Hoi, Cheryl Xueli Chan, Audrey SM Teo, Oscar Velazquez, Wee Yang Meah, Chiea Chuen Khor, Chin Thing Ong, Wendy W Soon, Patrick Tan, Pauline C Ng, Charles Chuah, Axel M Hillmer , S Tiong Ong

publication

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ALPK1 missense pathogenic variant in five families leads to ROSAH syndrome, an ocular multisystem autosomal dominant disorder

Genetics in Medicine, September 2019

Lloyd B Williams , Asif Javed , Amin Sabri , Denise J Morgan , Chad D Huff, John R Grigg, Xiu Ting Heng, Alexis J Khng, Iris HIM Hollink, Margaux A Morrison, Leah A Owen, Katherine Anderson, Krista Kinard, Rebecca Greenlees, Danica Novacic, H Nida Sen, Wadih M Zein, George M Rodgers, Albert T Vitale, Neena B Haider, Axel M Hillmer, Pauline C Ng, Anson Cheng, Linda Zheng, Mark C Gillies, Marjon van Slegtenhorst, P Martin van Hagen, Tom OAR Missotten, Gary L Farley, Michael Polo, James Malatack, Julie Curtin, Frank Martin, Susan Arbuckle, Stephen I Alexander, Megan Chircop, Sonia Davila, Kathleen B Digre, Robyn V Jamieson , Margaret M DeAngelis

publication

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De novo mutations in SMCHD1 cause Bosma arhinia microphthalmia syndrome and abrogate nasal development

Nature Genetics, September 2017

Christopher T Gordon , Shifeng Xue , Goekhan Yigit , Hicham Filali , Kelan Chen , Nadine Rosin, Koh-ichiro Yoshiura, Myriam Oufadem, Tamara J Beck, Ruth McGowan, Alex C Magee, Janine Altmueller, Camille Dion, Holger Thiele, Alexandra D Gurzau, Peter Nuernberg, Dieter Meschede, Wolfgang Muehlbauer, Nobuhiko Okamoto, Vinod Varghese, Rachel Irving, Sabine Sigaudy, Denise Williams, S Faisal Ahmed, Carine Bonnard, Mung Kei Kong, Ilham Ratbi, Nawfal Fejjal, Meriem Fikri, Siham Chafai Elalaoui, Hallvard Reigstad, Christine Bole-Feysot, Patrick Nitschke, Nicola Ragge, Nicolas Levy, Gökhan Tunçbilek, Audrey SM Teo, Michael L Cunningham, Abdelaziz Sefiani, Huelya Kayserili, James M Murphy, Chalermpong Chatdokmaiprai, Axel M Hillmer, Duangrurdee Wattanasirichaigoon, Stanislas Lyonnet, Frederique Magdinier, Asif Javed, Marnie E Blewitt, Jeanne Amiel , Bernd Wollnik , Bruno Reversade

publication editorial comment patent

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Phen-Gen: combining phenotype and genotype to analyze rare disorders

Nature Methods, September 2014

Asif Javed , Saloni Agrawal, Pauline C Ng

publication software

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Recombination networks as genetic markers in a human variation study of the Old World

Human genetics, April 2012

Asif Javed , Marta Melé , Marc Pybus, Pierre Zalloua, Marc Haber, David Comas, Mihai G Netea, Oleg Balanovsky, Elena Balanovska, Li Jin, Yajun Yang, GaneshPrasad ArunKumar, Ramasamy Pitchappan, Jaume Bertranpetit, Francesc Calafell , Laxmi Parida , Genographic Consortium

publication software publication patent

Contact

   Asif Javed
       Assistant Professor
       School of Biomedical Sciences
   Li Ka Shing Faculty of Medicine
       The University of Hong Kong
       5/F, Jockey Club Building for Interdisciplinary Research
       5 Sassoon Road, Hong Kong
   Tel: +852 2831 5395
   Email: javed@hku.hk
   Website: https://www.sbms.hku.hk/staff/asif-javed


HKJCIR