Our lab is focused on molecular biology, single-cell sequencing technologies and liquid biopsy in cancer. In particular, we are interested in pancreatic cancer diagnosis and treatment.
The lab is located at two sites: Lowy Cancer Research Centre (at University of New South Wales, UNSW) and Garvan Institute of Medical Research in Sydney, Australia. We are also affiliated to the Karolinska Institute in Stockholm, Sweden. We have access to cutting-edge instruments and facilities at UNSW and Garvan including next-generation sequencing, long-read sequencing (Nanopore Oxford Technology and PacBio), FACS, liquid handling robotics, automated micromanipulator, microfluidics, 3D printing, and microscopy. We collaborate closely with The Kinghorn Cancer Centre, The Ramaciotti Centre for Genomics, and Kinghorn Centre for Clinical Genomics.
We are interested in single-cell analysis to characterise the diversity of cell types in the human body. Studying a tissue in a single-cell resolution provides a more precise picture of its behaviour in health and disease.
We are also studying circulating tumour cells (CTCs), a diverse cell population that is released by solid tumours into the circulation in the form of single cells or cell clusters. CTCs can be used as a liquid biopsy to obtain information from tumours in a minimally invasive way. Our lab aims to investigate CTCs with single-cell technology to test whether they can potentially serve as a predictive/prognostic biomarker in solid cancers.
To reach these aims, we use the latest technology and when there is none, we develop it.
Single-cell multi-omics technology. Single-cell molecular analysis has been gaining momentum in various biological disciplines. We have developed some of the very popular single-cell transcriptomics technologies (also known as single-cell RNA sequencing) such as Smart-seq2, Small-seq and recently Smart-seq3. However, a method that detects and measures several molecular types in a single cell has been highly demanded. In this project, we develop a single-cell multi-omics technology to profile several molecular types including DNA, RNA, and proteins simultaneously in an individual cell.
Microfluidics for circulating tumour cells enrichment. Isolation and preparation of circulating tumour cells (CTCs) have been traditionally established for enumeration purposes and it is not optimised for single-cell RNA analysis; consequently, RNA content of CTCs can be compromised. Here, we aim to design a protocol for the isolation of viable CTCs from patients' blood using microfluidics to analyse with single-cell RNA sequencing.
Pancreatic cancer predictive biomarker. Pancreatic cancer is one of the world’s most lethal cancers, with a 5-year survival rate of just ~10%. It is often diagnosed very late when the tumour has spread out to the liver and other organs as metastases. Metastatic tumours cannot be removed by surgery and chemotherapy is the only option. The question is which chemotherapy drug works the best for each patient? To which drug will the tumour respond? In this project, we search for a molecular biomarker that predicts the tumour response to certain chemotherapy in each pancreatic cancer patient. We will examine CTCs and other markers.
Postdoc position in single-cell bioinformatics, 1 year with a possibility of extension, $100K (+ 9.5% superannuation & leave loading). please contact Dr Fabio Zanini E: firstname.lastname@example.org
We are always looking for enthusiastic and brilliant students and postdocs who care about science and improving cancer patients' lives. Please send us your CV if you are interested in joining us.
Honour students and clinical students interested in doing a PhD in molecular biology and pancreatic cancer are encouraged to contact us.
Publications and Patents
Faridani OR, Abdullayev I, Hagemann-Jensen M, Schell JP, Lanner F, Sandberg R.
Nat Biotechnol. 2016 Dec;34(12):1264-1266.
Hagemann-Jensen M, Abdullayev I, Sandberg R, Faridani OR.
Nat Protoc. 2018 Oct;13(10):2407-2424.
Larsson AJM, Johnsson P, Hagemann-Jensen M, Hartmanis L, Faridani OR, Reinius B, Segerstolpe Å, Rivera CM, Ren B, Sandberg R.
Nature. 2019 Jan;565(7738):251-254.
Methods and Compositions for cDNA Synthesis and Single-Cell Transcriptome Profiling Using Template Switching Reaction. (PCT/US2014/052233) 2015. This patent was licensed to Clontech/Takara for Smart-Seq V4 kit.
Methods of small-RNA transcriptome sequencing and applications thereof (PCT/US2017/037620).
Method and kit for preparing complementary DNA.(2019, application number: SE 1851672-4) 2019. This patent was also licensed to Clontech/Takara.
Omid Faridani , Group Leader, PhD the Karolinska Institute 2007. Postdoc Ludwig Institute for Cancer Research.
Mehdi Rafeie, Postdoc, PhD University of New South Wales 2018
Hossein Tavassoli, Postdoc, PhD Swinburne University of Technology 2020
Yun Cheah, Honour student
Nageswara Rao Boggavarapu, Postdoc, PhD the Karolinska Institute 2017.
Professor Kristina Gemzell Danielsson (Karolinska, Sweden)
Professor Claudia Spits (VIB, Belgium)
Professor Andres Salumet (University of Tartu, Estonia)
Associate Professor Joseph Powell (Garvan, Australia)
Professor John Pimanda (UNSW, Australia)
Dr Hamid Alinejad-Rokny (UNSW, Australia)
1. UNSW Lowy Cancer Research Centre, Cnr High and Botany St, Kensington 2033 NSW, Australia
2. Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst 2010 NSW, Australia
o.faridani [at] unsw.edu.au
o.faridani [at] garvan.org.au