Single nucleotide polymorphism-based genome-wide chromosome copy change, loss of heterozygosity, and aneuploidy in Barrett's esophagus neoplastic progression

Abstract

Chromosome copy gain, loss, and loss of heterozygosity (LOH) involving most chromosomes have been reported in many cancers; however, less is known about chromosome instability in premalignant conditions. 17p LOH and DNA content abnormalities have been previously reported to predict progression from Barrett's esophagus (BE) to esophageal adenocarcinoma (EA). Here, we evaluated genome-wide chromosomal instability in multiple stages of BE and EA in whole biopsies. Forty-two patients were selected to represent different stages of progression from BE to EA. Whole BE or EA biopsies were minced, and aliquots were processed for flow cytometry and genotyped with a paired constitutive control for each patient using 33,423 single nucleotide polymorphisms (SNP). Copy gains, losses, and LOH increased in frequency and size between early- and late-stage BE (P < 0.001), with SNP abnormalities increasing from <2% to >30% in early and late stages, respectively. A set of statistically significant events was unique to either early or late, or both, stages, including previously reported and novel abnormalities. The total number of SNP alterations was highly correlated with DNA content aneuploidy and was sensitive and specific to identify patients with concurrent EA (empirical receiver operating characteristic area under the curve = 0.91). With the exception of 9p LOH, most copy gains, losses, and LOH detected in early stages of BE were smaller than those detected in later stages, and few chromosomal events were common in all stages of progression. Measures of chromosomal instability can be quantified in whole biopsies using SNP-based genotyping and have potential to be an integrated platform for cancer risk stratification in BE.

Figure 1

Percent of probes across the genome with copy gain, loss and LOH in different stages of neoplastic progression measured in the 33K SNP array. * % SNP probes with LOH was calculated using only those SNPs that were heterozygous in the paired constitutive control.

Figure 2

Gain and loss size distribution of the four progression stages.

Figure 3

A. Distribution of informative SNPs with LOH (black bars) on chromosomes 1 to 5 (rows, oriented p-arm at the bottom and q-arm at the top of each chromosome) in individual samples from 42 patients (columns). Regions with no black bars represent either non-informative SNPs or no LOH. Patients are grouped along the x-axis into the four stages of neoplastic progression and the numbers along the x axis refer to individual patients. B. Genome wide LOH map of chromosomes 6 to 12 for individual samples (n=42). The organization is the same as in Figure 3A. C. Genome wide LOH map of chromosomes 13 to 22 of individual samples (n=42). The organization is the same is in Figure 3A.

Figure 3

A. Distribution of informative SNPs with LOH (black bars) on chromosomes 1 to 5 (rows, oriented p-arm at the bottom and q-arm at the top of each chromosome) in individual samples from 42 patients (columns). Regions with no black bars represent either non-informative SNPs or no LOH. Patients are grouped along the x-axis into the four stages of neoplastic progression and the numbers along the x axis refer to individual patients. B. Genome wide LOH map of chromosomes 6 to 12 for individual samples (n=42). The organization is the same as in Figure 3A. C. Genome wide LOH map of chromosomes 13 to 22 of individual samples (n=42). The organization is the same is in Figure 3A.

Figure 3

A. Distribution of informative SNPs with LOH (black bars) on chromosomes 1 to 5 (rows, oriented p-arm at the bottom and q-arm at the top of each chromosome) in individual samples from 42 patients (columns). Regions with no black bars represent either non-informative SNPs or no LOH. Patients are grouped along the x-axis into the four stages of neoplastic progression and the numbers along the x axis refer to individual patients. B. Genome wide LOH map of chromosomes 6 to 12 for individual samples (n=42). The organization is the same as in Figure 3A. C. Genome wide LOH map of chromosomes 13 to 22 of individual samples (n=42). The organization is the same is in Figure 3A.

Figure 4

Number of 0.5MB windows with chromosome lesions that reached statistical significance across patients in Early (BE early and BE instability) and Late (advanced BE and EA) stages of neoplastic progression. Light dots: The number of 0.5 MB windows that reached statistical significance in early stage (BE early and BE instability) samples only but were not significant in late stage samples. Intersection of dots and cross hatched: The number of events that reached statistical significance both in early stage (BE early and BE instability) and late stage (advanced BE and EA) samples. Cross hatched: The number of events that reached statistical significance in late stage (advanced BE and EA) samples only but were not significant in early stages.

Figure 5

ROC curve for separating advanced stages (advanced BE and EA) vs. early stages (BE or BE instability) using total genome wide LOH (AUC=0.91) or copy gain and loss (AUC=0.91).