Validation of DNA methylation biomarkers for diagnosis of acute lymphoblastic leukemia

Zac Chatterton, Daniel Burke, Kerry R. Emslie, Jeffery M. Craig, Jane Ng, David M. Ashley, Francoise Mechinaud, Richard Saffery, Nicholas C. Wong

Research output: Contribution to journalArticleResearchpeer-review

Abstract

BACKGROUND: DNA methylation biomarkers capable of diagnosis and subtyping have been found for many cancers. Fifteen such markers have previously been identified for pediatric acute lymphoblastic leukemia (ALL). Validation of these markers is necessary to assess their clinical utility for molecular diagnostics. Substantial efficiencies could be achieved with these DNA methylation markers for disease tracking with potential to replace patient-specific genetic testing. METHODS: We evaluated DNA methylation of promoter regions of TLX3 (T-cell leukemia homeobox) and FOXE3 (forkhead box E3) in bone marrow biopsies from 197 patients classified as leukemic (n=95) or clear of the disease (n=102) by MALDI-TOF. Using a single nucleotide extension assay (methylSABER), we tested 10 bone marrow biopsies collected throughout the course of patient chemotherapy. Using reference materials, diagnostic thresholds and limits of detection were characterized for both methods. RESULTS: Reliable detection of DNA methylation of TLX3 and FOXE3 segregated ALL from those clear of disease with minimal false-negative and false-positive results.The limit of detection withMALDI-TOFwas 1000-5000 copies of methylated allele. For methylSABER, the limit of detection was 10 copies of methylated TLX3, which enabled monitoring of minimal residual disease in ALL patients. CONCLUSIONS: Mass spectrometry procedures can be used to regionally multiplex and detect rare DNA methylation events, establish DNA methylation loci as clinically applicable biomarkers for disease diagnosis, and track pediatric ALL.

Original languageEnglish
Pages (from-to)995-1003
Number of pages9
JournalClinical Chemistry
Volume60
Issue number7
DOIs
Publication statusPublished - 2014
Externally publishedYes

Cite this

Chatterton, Zac ; Burke, Daniel ; Emslie, Kerry R. ; Craig, Jeffery M. ; Ng, Jane ; Ashley, David M. ; Mechinaud, Francoise ; Saffery, Richard ; Wong, Nicholas C. / Validation of DNA methylation biomarkers for diagnosis of acute lymphoblastic leukemia. In: Clinical Chemistry. 2014 ; Vol. 60, No. 7. pp. 995-1003.
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abstract = "BACKGROUND: DNA methylation biomarkers capable of diagnosis and subtyping have been found for many cancers. Fifteen such markers have previously been identified for pediatric acute lymphoblastic leukemia (ALL). Validation of these markers is necessary to assess their clinical utility for molecular diagnostics. Substantial efficiencies could be achieved with these DNA methylation markers for disease tracking with potential to replace patient-specific genetic testing. METHODS: We evaluated DNA methylation of promoter regions of TLX3 (T-cell leukemia homeobox) and FOXE3 (forkhead box E3) in bone marrow biopsies from 197 patients classified as leukemic (n=95) or clear of the disease (n=102) by MALDI-TOF. Using a single nucleotide extension assay (methylSABER), we tested 10 bone marrow biopsies collected throughout the course of patient chemotherapy. Using reference materials, diagnostic thresholds and limits of detection were characterized for both methods. RESULTS: Reliable detection of DNA methylation of TLX3 and FOXE3 segregated ALL from those clear of disease with minimal false-negative and false-positive results.The limit of detection withMALDI-TOFwas 1000-5000 copies of methylated allele. For methylSABER, the limit of detection was 10 copies of methylated TLX3, which enabled monitoring of minimal residual disease in ALL patients. CONCLUSIONS: Mass spectrometry procedures can be used to regionally multiplex and detect rare DNA methylation events, establish DNA methylation loci as clinically applicable biomarkers for disease diagnosis, and track pediatric ALL.",
author = "Zac Chatterton and Daniel Burke and Emslie, {Kerry R.} and Craig, {Jeffery M.} and Jane Ng and Ashley, {David M.} and Francoise Mechinaud and Richard Saffery and Wong, {Nicholas C.}",
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Chatterton, Z, Burke, D, Emslie, KR, Craig, JM, Ng, J, Ashley, DM, Mechinaud, F, Saffery, R & Wong, NC 2014, 'Validation of DNA methylation biomarkers for diagnosis of acute lymphoblastic leukemia' Clinical Chemistry, vol. 60, no. 7, pp. 995-1003. https://doi.org/10.1373/clinchem.2013.219956

Validation of DNA methylation biomarkers for diagnosis of acute lymphoblastic leukemia. / Chatterton, Zac; Burke, Daniel; Emslie, Kerry R.; Craig, Jeffery M.; Ng, Jane; Ashley, David M.; Mechinaud, Francoise; Saffery, Richard; Wong, Nicholas C.

In: Clinical Chemistry, Vol. 60, No. 7, 2014, p. 995-1003.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Validation of DNA methylation biomarkers for diagnosis of acute lymphoblastic leukemia

AU - Chatterton, Zac

AU - Burke, Daniel

AU - Emslie, Kerry R.

AU - Craig, Jeffery M.

AU - Ng, Jane

AU - Ashley, David M.

AU - Mechinaud, Francoise

AU - Saffery, Richard

AU - Wong, Nicholas C.

PY - 2014

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AB - BACKGROUND: DNA methylation biomarkers capable of diagnosis and subtyping have been found for many cancers. Fifteen such markers have previously been identified for pediatric acute lymphoblastic leukemia (ALL). Validation of these markers is necessary to assess their clinical utility for molecular diagnostics. Substantial efficiencies could be achieved with these DNA methylation markers for disease tracking with potential to replace patient-specific genetic testing. METHODS: We evaluated DNA methylation of promoter regions of TLX3 (T-cell leukemia homeobox) and FOXE3 (forkhead box E3) in bone marrow biopsies from 197 patients classified as leukemic (n=95) or clear of the disease (n=102) by MALDI-TOF. Using a single nucleotide extension assay (methylSABER), we tested 10 bone marrow biopsies collected throughout the course of patient chemotherapy. Using reference materials, diagnostic thresholds and limits of detection were characterized for both methods. RESULTS: Reliable detection of DNA methylation of TLX3 and FOXE3 segregated ALL from those clear of disease with minimal false-negative and false-positive results.The limit of detection withMALDI-TOFwas 1000-5000 copies of methylated allele. For methylSABER, the limit of detection was 10 copies of methylated TLX3, which enabled monitoring of minimal residual disease in ALL patients. CONCLUSIONS: Mass spectrometry procedures can be used to regionally multiplex and detect rare DNA methylation events, establish DNA methylation loci as clinically applicable biomarkers for disease diagnosis, and track pediatric ALL.

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JO - Clinical Chemistry

JF - Clinical Chemistry

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