Molecular Diagnostics 

Weprovide minimal residual disease testing for young people with leukaemia and conduct research to improve relapse prediction.

Group Leaders

What we do

Leukaemia (US spelling: leukemia), also known as blood cancer, makes up about one-third of childhood cancer. The most common type of leukaemia in children is acute lymphoblastic leukaemia (ALL). About 99 per cent of patients treated with chemotherapy for ALL initially go into remission, with the disappearance of their symptoms. However, about one in six of these children later relapse due to the persistence of small numbers of cancer cells in the body, referred to as minimal residual disease (MRD).

Almost all current clinical trials for patients with ALL include measurement of MRD levels to help clinicians determine the risk of relapse and to guide treatment decisions. We developed one of the best available methods to measure MRD in children with ALL and now provide MRD diagnostic testing for ALL patients enrolled on several clinical trials. We also carry out research to further improve our ability to determine each patient’s risk of relapse. 

Our Group’s broad aim is to conduct MRD testing as part of the routine clinical management of all children with ALL, allowing treatment to be tailored to the individual according to the level of disease remaining in their body. With this goal in mind, all aspects of our MRD testing are subject to quality assurance. Our work is dependent on close collaboration with children’s hospitals belonging to the Australian and Zealand Children’s Haematology and Oncology Group (ANZCHOG), which sponsors our international trials.

Research Projects

Molecular diagnostics for children with acute lymphoblastic leukaemia

Contact: A/Prof Rosemary Sutton, rsutton@ccia.org.au; Dr Michelle Henderson, mhenderson@ccia.org.au 

The diagnostic tests used at Children’s Cancer Institute to measure MRD rely on identifying unique genetic markers for each patient’s leukaemia and then developing highly sensitive real-time quantitative (RQ) PCR-based MRD tests to measure these markers. Markers can be measured even at very low levels, equivalent to one leukaemic blast cell in 100,000 normal bone marrow or blood cells.

Since 2002, MRD testing to measure early response to chemotherapy has been used to guide treatment decisions for children newly diagnosed with acute lymphoblastic leukaemia (ALL). While children with ALL usually need two years of chemotherapy, the level of disease present in the early stages (after 2 weeks, 1 month and 3 months) provides a good indication of whether standard chemotherapy will be sufficient for cure. This makes MRD levels an important aspect of the clinical trials in deciding patient treatment.

ANZCHOG Study 8 and Study 9 (AIEOP-BFM ALL 2009) clinical trials

Our first clinical trial using MRD testing, ANZCHOG Study 8 clinical trial, enrolled 607 children from Australia and New Zealand diagnosed between 2002 and 2011. Its main focus was to use MRD testing to identify patients with a high risk of relapse and to treat them more intensively in order to prevent relapse. Indeed, we doubled the survival of high-risk children with ALL on this trial.

As a result of this success, Study 8 was followed by the Study 9 trial which included 333 Australian children diagnosed between 2012 and 2016. This was an international trial comparing slightly different treatment options in 5000 patients in seven countries. Again, MRD testing was used to determine relapse risk, but the main focus of the trial was to reduce the toxicity of treatment while maintaining its effectiveness. In particular, Study 9 reduced chemotherapy for low risk patients, to reduce their risk of side-effects.

In the Study 9 trial, MRD testing was carried out after one month of treatment. Patients with five or more leukaemic cells per 10,000 were classed as ‘high risk’ and offered novel, more intensive chemotherapy and a bone marrow or cord blood transplant if a donor was available. Patients with low levels of MRD, the largest group, are usually defined as ‘medium risk’ and have an average rate of relapse close to 20 per cent. Patients in whom MRD levels are undetectable have greater than 95 per cent chance of cure and are usually defined as ‘standard risk’. 

Monitoring response to treatment in high risk patients

Children who have been assessed as ‘high-risk’ often continue on an MRD monitoring program, to check how their residual disease responds to the more intense chemotherapy used. The Study 8 clinical trial demonstrated that later test results are clinically valuable for high risk patients, so MRD tests were done and reported in real time to treating oncologists for high risk patients in Study 9.

 

The Study 8 trial used novel combinations of intensive chemotherapy for high risk patents designed by our clinical colleagues in the Sydney Children’s Hospitals Network. This treatment doubled the numbers of high risk patients cured, compared to earlier clinical trials, but caused serious toxic side effects in some patients. In Study 9, high risk patients were treated with a different intensive chemotherapy. The aim was to continue to improve the survival of high risk patients, but with less toxicity. The effectiveness of this strategy will be evaluated once all patients have been followed up for 5 years after diagnosis.

Research questions

Our collaborative studies on Study 8 trial samples showed we can do better in identifying high risk patients, by using MRD in combination with other molecular tests, particularly those testing for gene deletions and translocations associated with Ph-like disease.

This research provided evidence that other molecular tests used in combination with MRD testing could improve our prediction of risk. Those tests will be applied and could benefit new patients in the next trial – Study 10 (AIEOP-BFM ALL 2009) – which has recently started.

We are also investigating ‘next-generation sequencing’ technologies (whole-genome sequencing and computational analysis) as an approach to identify MRD markers for cases where we are unable to develop a test using a traditional marker.

Key clinical collaborators

Dr Draga Barbaric and Prof Glenn Marshall, Kids Cancer Centre, Sydney Children’s Hospital Randwick; Dr Luciano Dalla Pozza, Children’s Hospital Westmead; Dr Frank Alvaro, John Hunter Children’s Hospital; Prof Martin Schrappe iBFM, Kiel, Germany; Prof Deborah White, SAHMRI, Adelaide 

Funding

Substantial support for these trials over last 18 years has been provided from multiple sources including the NHMRC, Cancer Council NSW, Tour de Cure, and Leukemia Foundation.

Molecular diagnostics and research for relapsed acute lymphoblastic leukaemia

Contact: A/Prof Rosemary Sutton, rsutton@ccia.org.auDr Michelle Henderson, mhenderson@ccia.org.au

Since 2006, we have performed MRD testing for children with relapsed acute lymphoblastic leukaemia (ALL) at 8 children’s hospitals in Australia and New Zealand. The original ALLR3 trial also involved patients from the UK and The Netherlands. Its successors, IntReALL SR and IntReALL HR, are open to children with relapsed ALL from more than 20 countries.

Patients on the trial are each assigned to either the high or standard risk group based on their clinical features, including time to relapse, site of relapse and ALL subtype. MRD testing is being used in the standard-risk group to determine the best treatment option for each patient − chemotherapy alone (for patients with a very favourable MRD response after 5 weeks) or with a cord blood or bone marrow transplant. Patients in the high-risk group are all offered transplantation if a donor is available, with MRD levels monitored both before and after transplantation.

Historically, survival rates for relapsed ALL have been dismal, with only about 40 per cent of patients surviving for 5 years. The ALLR3 trial showed a significant improvement, with the three-year overall survival rate rising to 61 per cent. This was achieved mainly through a change in chemotherapy, with patients given Mitoxantrone instead of Idarubicin during the first week of treatment.   In the IntReALL SR trial, a new antibody therapy called Epratuzomab was used in combination with two of the best chemotherapy combinations, to see if it provided an extra benefit. The evidence showed that Epratuzomab was used safely but did not significantly improve cure rates, so the trial has been discontinued. The patients will be followed until 2023 to compare the toxicity and cure rates for the two different combination chemotherapy options. Research is particularly valuable in the context of relapse clinical trials, since additional tests and information collected for these patients enable factors contributing to patient survival to be identified.

Key external collaborators

Prof Vaskar Saha, Christie Hospital NHS Trust Manchester (ALLR3 trial chairman); Dr Julie Irving, University of Newcastle, UK; Dr Arend von Stackelberg and Dr Cornelia Eckert, Charite Hospital, Berlin and A/Prof Tamas Revesz, Adelaide Women and Children’s Hospital (lead ANZCHOG investigator)

Funding

MRD testing for relapsed ALL patients has been supported by different funding bodies over the years, including Sporting Chance Cancer Foundation (2008-2012), Cancer Council NSW and NHMRC.

Molecular diagnostics for babies with acute lymphoblastic leukaemia (Interfant 06 and Blinfant trials)

Contact: A/Prof Rosemary Sutton, rsutton@ccia.org.auDr Michelle Henderson, mhenderson@ccia.org.au

Since 2005, we have performed MRD testing for infants with acute lymphoblastic leukaemia (ALL) diagnosed in Australia or New Zealand. This is a small group of 4-8 patients per year who are very difficult to treat, especially those with mixed-lineage leukaemia (MLL) gene rearrangements.  A special form of MRD testing has been developed to measure MLL leukaemia in infants, where it is the most common marker, as well as some cases of children and adults with ALL, mixed phenotype acute leukaemia, or acute myeloid leukaemia with MLL gene rearrangement.

Through our collaboration with the leading German laboratory, we are able to provide MLL MRD testing. In conjunction with other laboratories of the EuroMRD group, we established a system for MLL MRD quality assurance to ensure uniformity of testing procedures for the international clinical trial.

In the Interfant 06 trial (2009-2019), MRD testing was used to assess how well the babies with ALL responded to two different types of chemotherapy. Our team performed the tests for Australian and Zealand Children’s Haematology and Oncology Group (ANZCHOG) patients.  For the majority of patients, those in the medium-risk group, these tests determined whether they received chemotherapy alone (if MRD levels are low) or chemotherapy followed by a bone marrow or cord blood transplant. Unfortunately, not all clinical trials provide clear cut answers and new chemotherapy tested in this trial was not found to be any better than the existing combination.

We have since started diagnostic support for a new early phase trial for babies with B-ALL, evaluating an immunotherapy used in combination with chemotherapy that we hope will prove more effective and less toxic.

Key external collaborators

Professor Rob Pieters, Erasmus Medical Centre, The Netherlands (trial chairman); Prof Rolf Marschalek, Frankfurt, Germany; Dr Andrew Moore, Lady Cilento Hospital, Brisbane; Dr Rishi Kotecha, Princess Margaret Hospital, Perth (lead ANZCHOG investigator).

Funding

Support for our research and MRD testing for infant trials has been provided over the years by Sporting Chance Cancer Foundation and The Reuben Pelerman Benevolent Foundation.

Molecular diagnostics for adults with acute lymphoblastic leukaemia (ALL6, Bombora, ALL8, ALL9)

Contact: A/Prof Rosemary Sutton, rsutton@ccia.org.auDr Michelle Henderson, mhenderson@ccia.org.au

Several international trials have shown that adolescents treated with paediatric ALL protocols have better outcomes than those treated on adult ALL protocols. Based on these results, the Australian Leukaemia and Lymphoma Group enrolled 85 newly diagnosed ALL patients on the ALL6 clinical trial in 2012 to 2018 for patients aged 15-40 years at 16 hospitals around Australia, for which Children’s Cancer Institute provided MRD testing. The trial intensified chemotherapy but reduced the number of transplants for adults with ALL.

A parallel research project called ‘BOMBorA – Biomarkers and MRD’ was conducted on patients being referred for MRD testing outside the ALL6 trial, including some patients in the 40-70 year-old age bracket. This project has established that benefits from MRD testing apply to patients of all ages, from birth to 70 years of age.

The ALL6 trial and BOMBorA were widely supported by haematologists treating adults with ALL of all ages, and as a result two more trials are now being conducted. Both of these trials are evaluating a new immunotherapy used in combination with chemotherapy.

The ALL8 trial is for patients over 40 years of age and the ALL9 trial is for adolescents and young adults (15-40 years).

While improving survival of adults with cancer is not usually a focus of research at Children’s Cancer Institute, we are pleased to be able to apply our expertise to support trials such as ALL8 and ALL9 and to help their patients.

Key external collaborators

Dr Matthew Greenwood, Royal North Shore Hospital (ALL6 and ALL9 trial chairman), Dr Shaun Fleming, The Alfred Hospital (ALL8 trial chairman)

Funding

Australian Leukemia Lymphoma Group

Molecular diagnostics and research for transplant patients (FORUM trial)

Contact: A/Prof Rosemary Sutton, rsutton@ccia.org.au

As part of the Study 8 clinical trial and also the BOMBorA project, we have shown the value of measuring MRD levels before and after transplant in predicting cure. Patients with MRD persisting after transplant have a high chance of relapsing, so some interventions are being trialled to prevent relapse.

The ANZCHOG-sponsored ALLSCTped 2010 FORUM trial was an international effort to reduce the side-effects of treatment in transplant patients by replacing total body irradiation with ablative chemotherapy in some patients.  In all, 21 patients from Australia and New Zealand were enrolled and about 600 internationally.

Unfortunately, the relapse rate was higher for patients who did not receive total body irradiation, so enrolment of patients stopped. The trial follow up continues to compare the longer term side-effects.

MRD testing before and immediately after transplant was a key part of the trial. In addition, patients could be enrolled on an extension called ‘EMAT – Evaluation of MRD After Transplant’ that examined the value of extended monitoring with intervention when MRD is detected.

Key external collaborators

Prof Peter Shaw, Children’s Hospital Westmead; Prof Tracey O’Brien, Sydney Children’s Hospital Randwick

Funding

Cancer Australia pdCCRS grants

Team

Diagnostics Manager

Nicola Venn

Senior Research Assistant

Tamara Law

Senior Technical Officer

Jodie Giles

Research Assistants

Erika Ong

Libby Huang

Dan Chen

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