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Anna Schuh

Application of nanopore sequencing in clinical haematology

About Anna Schuh

Professor Schuh completed academic and clinical haematology training in Oxford and in 2006, she was appointed clinical lead for haematology laboratories, including molecular diagnostics, and has also been the clinical lead for chronic lymphocytic leukaemia and other lymphoproliferative disorders for the NHS Thames Valley Cancer Network. Over the past twelve years she has led over 30 early and late phase clinical trials in leukaemia as a principle or national chief investigator. A number of these led to NICE approvals and have changed clinical practice for patients in the UK and worldwide. As a result, she was recently appointed as the Chair of Chronic Lymphocytic Leukaemia Research in the UK by the National Cancer Research Institute. In addition to other national and international roles, she has also chaired the UK CLL Forum since 2016 that promotes training and education, and she has led the UK's guidelines writing group for CLL Therapy on behalf of the British Society of Haematology. Her second research interest is with the development, evaluation and implementation of new technologies for Precision Diagnostics, especially genomics. Her group published the first ever longitudinal study of the changes in the genomic landscape of patients undergoing treatment for leukaemia. She is the lead for the Genomics England Clinical Interpretation Partnership for haematological malignancies. Professor Schuh has received grants from the NIHR, Wellcome Trust, Technology Strategy Board, Cancer Research UK and Bloodwise and she has authored or co-authored over 80 peer-reviewed publications in the last five years.

Abstract

Blood cancers are together the 5th most common cancer and many patients are young adults. Besides, the most common cancers of childhood worldwide are acute lymphoblastic leukaemia and endemic Burkitt’s Lymphoma. Six of the 10 most lucrative cancer drugs are prescribed for haematological malignancies ($55.6billion by 2025). Their diagnosis requires a microscope and DNA-based precision diagnostics. But precision diagnostics is not always about identifying a simple base pair change, and requires the detection of all different types of mutations from one single (often small) patient sample. Examples of where DNA-based diagnostics are critical will be given and include all leukaemias and an increasing number of lymphomas. Their detection is recommended by the WHO classification of haematological malignancies. For example, the NHS test directory includes 177 different genetic aberrations.


The problem is that current multimodality testing in diagnostics laboratories is inadequate to deal with this demand on testing. Many of the conventional single gene assays lack sensitivity, speed and precision. Illumina whole genome sequencing (WGS) of tumour and paired germline has the potential to reveal all types of different mutations and global measures across the genome, but it is limited by the small fragment size and the need for large and expensive equipment. As part of the Genomics England Chronic Lymphocytic leukaemia Pilot have used information from Illumina WGS from 400 patients to develop an improved response prediction tool for chemoimmunotherapy that predicts patients who will be cured (manuscript in preparation). An alternative way specifically for diagnostics, is to combine targeted deep sequencing and error correction with shallow whole genome sequencing using the MinION. This method and variations of it can be applied globally in haematology. For example, the most common inherited anaemias, the haemoglobinopathies, are characterised by 1700 SNVs/indels and deletions across three genes. The most common of these, sickle cell disease, occurs in sub-Saharan Africa. About 10% of patients require confirmatory diagnosis by genetics. Life-saving therapies are available for this disease, and knowledge of the presence of the condition in the fetus could significantly streamline neonatal screening programmes around the world. We have clinically validated a proprietary method for non-invasive testing for sickle cell disease from maternal plasma (pre-published in BioRxiv) and have also developed a nanopore-based test for diagnosing haemoglobinopathies from germline DNA without the need for PCR amplification.


Finally, plasma-derived DNA can also be used in other clinical indications in sub-Saharan Africa. The most common childhood cancer in the region is endemic Burkitt’s lymphoma. This is caused by EBV infection in early childhood. With simple treatment, over 90% of patients can be cured. And treatment is free of charge in all African countries affected. Currently, over 90% of kids die. This is because children present late and are not diagnosed once in hospital because there is lack of trained surgeon and pathologists to establish the diagnosis from an invasive biopsy across the region. We are now clinically validating a non-invasive method to diagnose this type of lymphoma from the blood using a combination of tumour and virus sequencing.


In conclusion: haematological diseases have always spearheaded innovations and discoveries in medicine, in particular genetics. Precision medicine is a reality for an increasing number of patients with blood diseases from targeted small molecules in leukaemias and lymphomas to gene therapy in the inherited blood diseases. The next step is to leapfrog diagnostics technologies and to introduce these advances globally as expensive cancer therapies are coming off patent and are increasingly available and on the WHO list of essential medicines. Ultimately, this approach will achieve a huge impact for a large number of patients world-wide.
 

Anna Schuh

Anna Schuh

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