Table 1.
Cox regression analysis: Hazard Ratio (HR) for the development of arsenic-induced skin lesions by presence or absence of genomic deletions in different chromosomal locations. Combined analysis of total 2171 HEALS participants. Top genomic segments are sorted by chromosome
| CNV genomic coordinates (GRCh37/hg19) | cytoband | length (bps) | Freq_Del | Nearest Gene | Distance to Nearest Gene (bps)b | HR (gene)a | 95% CI (gene) | p-value | Bonferroni p-value | Nearest reported CNV in DGV database | Distance to Nearest reported CNV (bps)c | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| chr2:104,543,558-104,558,092 | 2q12.1 | 14,535 | 18.06% | RP11-76I14.1 (+) | 0 | 1.70 | 1.36 | 2.13 | 4.35E-06 | 0.005 | chr2:104,593,605..104760102 | 35,513 |
| chr2:104,558,092-104,568,449 | 2q12.1 | 10,358 | 18.06% | RP11-76I14.1 (+) | 0 | 1.70 | 1.36 | 2.13 | 4.11E-06 | 0.005 | chr2:104,593,605..104760102 | 25,156 |
| chr2:104,573,423-104,581,271 | 2q12.1 | 7849 | 18.70% | RP11-76I14.1 (+) | 0 | 1.67 | 1.34 | 2.10 | 7.05E-06 | 0.008 | chr2:104,593,605..104760102 | 12,334 |
| chr3:102,717,330-102,770,447 | 3q12.3 | 53,118 | 6.54% | RNU1-43P (+) | 108,357 | 2.11 | 1.53 | 2.91 | 5.08E-06 | 0.006 | chr3:102,743,602..102752706 | 0 |
| chr5:164,917,182-164,925,967 | 5q34 | 8786 | 5.62% | CTC-535 M15.2 (+) | 0 | 2.15 | 1.55 | 2.98 | 4.62E-06 | 0.005 | chr5:164,849,860..164874815 | 42,367 |
| chr5:164,925,967-164,939,621 | 5q34 | 13,655 | 5.80% | CTC-535 M15.2 (+) | 0 | 2.11 | 1.52 | 2.91 | 6.55E-06 | 0.007 | chr5:164,849,860..164874815 | 51,152 |
| chr5:164,939,621-164,956,122 | 5q34 | 16,502 | 5.85% | CTC-535 M15.2 (+) | 0 | 2.10 | 1.52 | 2.90 | 7.39E-06 | 0.008 | chr5:164,849,860..164874815 | 64,806 |
| chr5:164,956,122-164,973,175 | 5q34 | 17,054 | 5.62% | CTC-535 M15.2 (+) | 0 | 2.14 | 1.54 | 2.97 | 5.08E-06 | 0.006 | chr5:164,849,860..164874815 | 81,307 |
| chr7:151,708,046-151,713,498 | 7q36.1 | 5453 | 8.15% | GALNTL5 (+) | 0 | 1.88 | 1.40 | 2.53 | 3.07E-05 | 0.035 | chr7:151,794,196..151797877 | 80,698 |
| chr7:151,713,498-151,719,077 | 7q36.1 | 5580 | 7.97% | GALNTL5 (+) | 0 | 1.87 | 1.39 | 2.52 | 4.25E-05 | 0.048 | chr7:151,794,196..151797877 | 75,119 |
| chr7:62,764,248-62,830,796 | 7q11.21 | 66,549 | 15.98% | VN1R31P (−) | 0 | 1.69 | 1.34 | 2.14 | 1.19E-05 | 0.014 | chr7:62,830,337..62835635 | 0 |
| chr7:62,835,371-62,889,537 | 7q11.21 | 54,167 | 15.80% | RP11-73B2.2 (−) | 0 | 1.70 | 1.34 | 2.15 | 1.01E-05 | 0.012 | chr7:62,864,828..62908102 | 0 |
| chr7:62,889,537-62,990,599 | 7q11.21 | 101,063 | 16.12% | PHKG1P2 (+) | 0 | 1.70 | 1.35 | 2.15 | 9.35E-06 | 0.011 | chr7:62,985,473..63249879 | 0 |
| chr8:14,696,759-14,702,931 | 8p22 | 6173 | 11.98% | SGCZ (−) | 0 | 1.73 | 1.35 | 2.23 | 2.10E-05 | 0.024 | chr8:14,697,130..14719288 | 0 |
| chr8:14,702,931-14,710,309 | 8p22 | 7379 | 12.16% | SGCZ (−) | 0 | 1.72 | 1.33 | 2.21 | 2.65E-05 | 0.030 | chr8:14,697,130..14719288 | 0 |
| chr8:14,720,385-14,737,759 | 8p22 | 17,375 | 5.62% | CTD-2023 J5.1 (−) | 0 | 2.11 | 1.53 | 2.89 | 4.04E-06 | 0.005 | chr8:14,680,345..14849094 | 0 |
| chr9:40,824,400-40,839,148 | 9p13.1 | 14,749 | 11.05% | ZNF658 (−) | 0 | 1.83 | 1.37 | 2.44 | 3.96E-05 | 0.045 | chr9:40,832,700..41365793 | 0 |
| chr9:40,857,839-40,876,494 | 9p13.1 | 18,656 | 13.54% | BX664608.1 (+) | 44,448 | 1.72 | 1.33 | 2.23 | 3.88E-05 | 0.044 | chr9:40,832,700..41365793 | 0 |
| chr9:40,876,494-40,895,281 | 9p13.1 | 18,788 | 13.36% | BX664608.1 (+) | 63,103 | 1.74 | 1.34 | 2.25 | 3.40E-05 | 0.039 | chr9:40,832,700..41365793 | 0 |
| chr11:55,900,420-55,952,826 | 11q12.1 | 52,407 | 11.79% | OR5J2 (+) | 0 | 1.73 | 1.34 | 2.24 | 3.10E-05 | 0.035 | chr11:55,962,241..55976332 | 9415 |
| chr11:55,952,826-55,965,828 | 11q12.1 | 13,003 | 11.29% | OR8V1P (−) | 0 | 1.75 | 1.34 | 2.26 | 2.84E-05 | 0.032 | chr11:55,962,241..55976332 | 0 |
| chr15:23,938,636-23,943,758 | 15q11.2 | 5123 | 7.46% | NDN (−) | 6185 | 1.95 | 1.42 | 2.67 | 3.73E-05 | 0.042 | chr15:23,973,556..23974955 | 29,798 |
| chr15:29,061,004-29,089,826 | 15q13.1 | 28,823 | 21.10% | GOLGA6L7P (−) | 0 | 1.71 | 1.32 | 2.21 | 3.87E-05 | 0.044 | chr15:29,066,490..29069430 | 0 |
| chr15:29,089,826-29,154,407 | 15q13.1 | 64,582 | 14.14% | APBA2 (+) | 0 | 1.80 | 1.36 | 2.39 | 3.64E-05 | 0.041 | chr15:29,093,623..29096097 | 0 |
aHazard Ratio if genomic deletion is present; Cox regression model includes genomic segment, gender, age, UACR - all dichotomized variables. The linc RNA regions are shown in bold font. b genomic segments with “Distance to nearest gene” >0 indicates that the segment doesn’t cover the gene, but it is close to that gene. c genomic segments with “Distance to nearest reported CNV” = 0 indicates that the identified CNV overlaps with known CNV repoted in the DGV database