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Open Access Technical advance

A new method to detect loss of heterozygosity using cohort heterozygosity comparisons

Michael R Green12, Paul Jardine3, Peter Wood4, Jeremy Wellwood5, Rod A Lea16, Paula Marlton7 and Lyn R Griffiths12*

Author Affiliations

1 Genomics Research Centre, Griffith Institute for Health & Medical Research, Griffith University, Parklands Drive, Southport, Queensland, Australia

2 Griffith Medical Research College, a joint program of Griffith University and the Queensland Institute of Health and Medical Research, QIMR, Herston Road, Herston, Queensland, Australia

3 Research Computing Services, Griffith University, Parklands Drive, Southport, Queensland, Australia

4 The Prince Charles Hospital, Queensland Health, Rode Road, Chermside, Queensland, Australia

5 Gold Coast Hospital, Queensland Health, Nerang Road, Southport, Queensland, Australia

6 Institute of Environmental Science and Research, Kenepuru Drive, Porirua, New Zealand

7 Princess Alexandra Hospital, Queensland Health, Ipswitch Road, Woloongabba, Queensland, Australia

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BMC Cancer 2010, 10:195  doi:10.1186/1471-2407-10-195

Published: 12 May 2010

Abstract

Background

Loss of heterozygosity (LOH) is an important marker for one of the 'two-hits' required for tumor suppressor gene inactivation. Traditional methods for mapping LOH regions require the comparison of both tumor and patient-matched normal DNA samples. However, for many archival samples, patient-matched normal DNA is not available leading to the under-utilization of this important resource in LOH studies. Here we describe a new method for LOH analysis that relies on the genome-wide comparison of heterozygosity of single nucleotide polymorphisms (SNPs) between cohorts of cases and un-matched healthy control samples. Regions of LOH are defined by consistent decreases in heterozygosity across a genetic region in the case cohort compared to the control cohort.

Methods

DNA was collected from 20 Follicular Lymphoma (FL) tumor samples, 20 Diffuse Large B-cell Lymphoma (DLBCL) tumor samples, neoplastic B-cells of 10 B-cell Chronic Lymphocytic Leukemia (B-CLL) patients and Buccal cell samples matched to 4 of these B-CLL patients. The cohort heterozygosity comparison method was developed and validated using LOH derived in a small cohort of B-CLL by traditional comparisons of tumor and normal DNA samples, and compared to the only alternative method for LOH analysis without patient matched controls. LOH candidate regions were then generated for enlarged cohorts of B-CLL, FL and DLBCL samples using our cohort heterozygosity comparison method in order to evaluate potential LOH candidate regions in these non-Hodgkin's lymphoma tumor subtypes.

Results

Using a small cohort of B-CLL samples with patient-matched normal DNA we have validated the utility of this method and shown that it displays more accuracy and sensitivity in detecting LOH candidate regions compared to the only alternative method, the Hidden Markov Model (HMM) method. Subsequently, using B-CLL, FL and DLBCL tumor samples we have utilised cohort heterozygosity comparisons to localise LOH candidate regions in these subtypes of non-Hodgkin's lymphoma. Detected LOH regions included both previously described regions of LOH as well as novel genomic candidate regions.

Conclusions

We have proven the efficacy of the use of cohort heterozygosity comparisons for genome-wide mapping of LOH and shown it to be in many ways superior to the HMM method. Additionally, the use of this method to analyse SNP microarray data from 3 common forms of non-Hodgkin's lymphoma yielded interesting tumor suppressor gene candidates, including the ETV3 gene that was highlighted in both B-CLL and FL.