Genome-wide analysis of survival in early-stage non-small-cell lung cancer

Abstract

Purpose: Lung cancer, of which 85% is non-small-cell (NSCLC), is the leading cause of cancer-related death in the United States. We used genome-wide analysis of tumor tissue to investigate whether single nucleotide polymorphisms (SNPs) in tumors are prognostic factors in early-stage NSCLC.

Patients and methods: One hundred early-stage NSCLC patients from Massachusetts General Hospital (MGH) were used as a discovery set and 89 NSCLC patients collected by the National Institute of Occupational Health, Norway, were used as a validation set. DNA was extracted from flash-frozen lung tissue with at least 70% tumor cellularity. Genome-wide genotyping was done using the high-density SNP chip. Copy numbers were inferred using median smoothing after intensity normalization. Cox models were used to screen and validate significant SNPs associated with the overall survival.

Results: Copy number gains in chromosomes 3q, 5p, and 8q were observed in both MGH and Norwegian cohorts. The top 50 SNPs associated with overall survival in the MGH cohort (P < or = 2.5 x 10(-4)) were selected and examined using the Norwegian cohort. Five of the top 50 SNPs were validated in the Norwegian cohort with false discovery rate lower than 0.05 (P < .016) and all five were located in known genes: STK39, PCDH7, A2BP1, and EYA2. The numbers of risk alleles of the five SNPs showed a cumulative effect on overall survival (P(trend) = 3.80 x 10(-12) and 2.48 x 10(-7) for MGH and Norwegian cohorts, respectively).

Conclusion: Five SNPs were identified that may be prognostic of overall survival in early-stage NSCLC.

Fig 1.

(A) Prevalence (%) and its (B) false discovery rate (q values) of patients with copy number ≥ 2.7 (red) and ≤ 1.3 (blue) in two cohorts, respectively. The x-axis represents the positions in genome/chromosomes, and the y-axis represents the prevalence and -log₁₀ (q values).

Fig 2.

Kaplan-Meier survival estimates of overall survival among the Massachusetts General Hospital (MGH) and Norwegian cohorts and relapse-free survival among the MGH cohort according to the numbers of risk alleles of the five single nucleotide polymorphisms (rs10176669, rs4438452, rs12446308, rs13041757, and rs10517215) in (A-C) total, (D-F) stage IA, (G-I) stage IB, and (J-L) stage II subjects.

Fig A1.

Kaplan-Meier survival estimates of overall survival among the Massachusetts General Hospital and Norwegian cohorts and relapse-free survival among the MGH cohort according to the numbers of risk alleles of the five single nucleotide polymorphisms (rs10176669, rs4438452, rs12446308, rs13041757, and rs10517215) in (A-C) adenocarcinoma and (D-F) squamous cell carcinoma.

Fig A2.

(A, B) Linkage disequilibrium structure of STK39 locating at 2q24.3. (C) The P values of the association of single nucleotide polymorphisms (SNPs) of A2BP1 around rs12446308 (16p13.3) with the overall survival and (D) the corresponding linkage disequilibrium (LD) structure. (E) The P values and the (F) LD plot of EYA2 around rs13041757 (20q13.1). (G, H) SNPs of PCDH7 around rs10517215 and rs1374653 (4p15). (A, C, E, G) The red points represent P < .01, whereas blue points represent P ≥ .01. (B, D, F, H) Boxe are shaded according to the standardized disequilibrium coefficient and the numbers in the boxes represent the disequilibrium coefficient, D', where the empty boxes mean the D' = 1.

Fig A2.

(A, B) Linkage disequilibrium structure of STK39 locating at 2q24.3. (C) The P values of the association of single nucleotide polymorphisms (SNPs) of A2BP1 around rs12446308 (16p13.3) with the overall survival and (D) the corresponding linkage disequilibrium (LD) structure. (E) The P values and the (F) LD plot of EYA2 around rs13041757 (20q13.1). (G, H) SNPs of PCDH7 around rs10517215 and rs1374653 (4p15). (A, C, E, G) The red points represent P < .01, whereas blue points represent P ≥ .01. (B, D, F, H) Boxe are shaded according to the standardized disequilibrium coefficient and the numbers in the boxes represent the disequilibrium coefficient, D', where the empty boxes mean the D' = 1.

Fig A2.

(A, B) Linkage disequilibrium structure of STK39 locating at 2q24.3. (C) The P values of the association of single nucleotide polymorphisms (SNPs) of A2BP1 around rs12446308 (16p13.3) with the overall survival and (D) the corresponding linkage disequilibrium (LD) structure. (E) The P values and the (F) LD plot of EYA2 around rs13041757 (20q13.1). (G, H) SNPs of PCDH7 around rs10517215 and rs1374653 (4p15). (A, C, E, G) The red points represent P < .01, whereas blue points represent P ≥ .01. (B, D, F, H) Boxe are shaded according to the standardized disequilibrium coefficient and the numbers in the boxes represent the disequilibrium coefficient, D', where the empty boxes mean the D' = 1.

Fig A2.

(A, B) Linkage disequilibrium structure of STK39 locating at 2q24.3. (C) The P values of the association of single nucleotide polymorphisms (SNPs) of A2BP1 around rs12446308 (16p13.3) with the overall survival and (D) the corresponding linkage disequilibrium (LD) structure. (E) The P values and the (F) LD plot of EYA2 around rs13041757 (20q13.1). (G, H) SNPs of PCDH7 around rs10517215 and rs1374653 (4p15). (A, C, E, G) The red points represent P < .01, whereas blue points represent P ≥ .01. (B, D, F, H) Boxe are shaded according to the standardized disequilibrium coefficient and the numbers in the boxes represent the disequilibrium coefficient, D', where the empty boxes mean the D' = 1.