Table 1 Prevalence of 9p24.1 amplifications in renal cell carcinomas

The Cancer Genome Atlas [31,32,33,34]

Whole exome next generation sequencing assay

3/533 (0.6%) clear cell renal cell carcinoma

0/66 chromophobe renal cell carcinoma

0/280 papillary renal cell carcinoma

[Total cohort: 3/879 (0.3%) renal cell carcinoma]

See Table 2 (cases 6, 11, and 12) for details

Malouf et al. [36]

255 gene hybrid capture-based next generation sequencing assay

2/26 (7.7%) renal cell carcinoma with sarcomatoid transformation

Case 1: sarcomatoid renal cell carcinoma (LRP1B c.10638G>C, TP53 c.395A>T,

PTEN c.209+1G>C,

JAK2/CD274 amplification, VHL deletion)

Case 2: unclassified renal cell carcinoma (CCND1/ MDM4/RPTOR/JAK2 amplification)

Casuscelli et al. [35]

MSK-IMPACT next generation sequencing assay; (341–410 gene hybrid capture-based assay)

2/60 (3.3%) chromophobe renal cell carcinoma

Case 1: included in Discovery Cohort

(see case 3 in Table 2)

Case 2: see case 13 in Table 2

Goodman et al. [3]

Foundation One next generation sequencing assay (315-405 gene hybrid capture-based assay)

4/66 (6.1%) renal cell carcinoma with sarcomatoid transformation

[Total Cohort: 4/766 (0.5%) renal cell carcinoma, not otherwise specified]

Not reported

Discovery cohort

MSK-IMPACT next generation sequencing assay

(341–468 gene hybrid capture-based assay, n = 573);

Fluorescence in situ hybridization (whole slide section)

JAK2/INSL6 (n = 26),

PD-L1/PD-L2 (n = 2);

Immunohistochemistry:

PD-L1/PD-L2/PD1/pSTAT3 (n = 6)

5/33 (15.1%) renal cell carcinoma with sarcomatoid transformation

(13 cases profiled by MSK-IMPACT,

20 cases screened by JAK2/INSL6 fluorescence in situ hybridization)

[Total cohort: 5/593 (0.8%) renal cell carcinoma]

See Table 2 (cases 1–5) for details

Present study

Validation cohort

Fluorescence in situ hybridization (tissue microarray)

JAK2/INSL6 (n = 398)

Fluorescence in situ hybridization (whole slide section)

JAK2/INSL6 (n = 4)

PD-L1/PD-L2 (n = 1)

Immunohistochemistry:

PD-L1/PD-L2 (n = 4)

4/127 (3.1%) renal cell carcinoma with sarcomatoid transformation

0/271 non-sarcomatoid renal cell carcinoma

[Total cohort: 4/398 (1.0%) renal cell carcinoma]

See Table 2 (cases 7–10) for details

Present study