Table 3

FISH panel and virtual karyotype results for 22 morphologically challenging renal tumors

Sample ID

Histologic Diagnosis

FISH

Virtual Karyotype

Virtual Karyotype Interpretation

Array Result vs. Final Diagnosis*

Outcome

Months Follow up


MC01

Low grade neoplasm, favor oncocytoma

Not done

-1, -14, -21

Oncocytoma

Confirms

No evidence of tumor

9


MC02

Low grade neoplasm, favor oncocytoma

Not done

del(10)(p11.23-p14)

Oncocytoma

Confirms

Disease status Unknown

1


MC09

Eosinophilic epithelial tumor morphologically consistent with eosinophilic renal cell carcinoma

-1 (44%), -2 (52%), -7 (38%), and -17 (88%)

-1, -1, -2, -3, +5, UPD 6, +7, -9, -9, -10p, -10p, del(10)(q24.33-qter), -11, -11, +12, -13,-13, +15(q22.2-qter), +16p, -17p, -17p, -17p, -17q, -17q, -18, +19, -21, -21, -22, -22, -22 | [inferred tetrasomy]

Mixed pattern CRCC/CHRCC = Unclassified

Novel pattern

Local & regional lymph node recurrence 52 months after nephrectomy Alive at last F/U

69


MC10

Oncocytic renal neoplasm, favor carcinoma

-1 (51%), 2 failed, +7 (21%), +7+7 (8%), +17 (30%) and intermediate -17(28%)

-1, -14

Oncocytoma

SNP diagnostic

No evidence of tumor

30


MC11

Renal cell carcinoma, clear cell type with focal granular (eosinophilic) morphology

CHRCC area: +2 (75%) with intermed -1, -7, -17; CRCC area: -1, -2, -17 (34%, 36%, 30%)

UPD(3)(p14.1-p13.2)

Clear Cell RCC

Confirms

No evidence of tumor

33


MC12

Eosinophilic variant of clear cell renal carcinoma with papillary features.

-2 (31%), -7 (37%), -17 (97%)

del(4)(p15.1-pter), +5(q21.3-qter), +9p(UPD), del(11)(q13.3-qter), +12, +16, del(17p), +17(q21.32-qter), +17(q21.32-qter), +20, -22

Novel, not consistent with clear cell

Novel pattern

Never disease free. Deceased

2


MC13

Oncocytic renal cell carcinoma, most suggestive of eosinophilic variant of conventional clear cell carcinoma

-1 (97%), -2 (83%), -7 (70%), and -17 (97%)

UPD(3)(p12.2-p24.1)

Clear Cell RCC

Confirms

No evidence of tumor

3


MC14

Chromophobe renal cell carcinoma

-1 (48%), -2 (50%), -7 (56%), and -17 (47%)

No detectable chromosomal abnormalities

Oncocytoma

Discrepant

No evidence of tumor

29


MC15

Renal cell carcinoma with morphologic features consistent with eosinophilic variant of clear cell carcinoma

-2 (37%), -7 (45%), -17 intermediate (20%)

del(1)(p32.3-pter), del(3)(p12.2-pter)

Clear Cell RCC

Confirms

Never disease free. Deceased

19


MC16

Oncocytic renal epithelial neoplasm, favor chromophobe renal cell carcinoma with eosinophilic morphology

-1(48%), -2 (40%), -7 (36%), and -17 (42%)

-1p, -9q, +12, -18, -21

Oncocytoma (novel)

Discrepant

No evidence of tumor

30


MC18

Low grade carcinoma with myxoid matrix and spindle and tubular architecture

-1 (85%), -2 (67%), -7 (37%), and -17 (73%)

-1, -4, -6, -8, -9, -13, -14, -15, -17, -22

MTSCC

Confirms

No evidence of tumor

19


MC19

Renal cell carcinoma with morphologic features of a chromophobe renal cell carcinoma. Multiple other tumors (2 papillary, 2 clear cell)

-1 (38%), -2 (42%), -7 (33%). 17 failed.

-3p, +3q, +7, del(9)(p13.2-p22.3)

Clear Cell RCC

Confirms

No evidence of tumor

21


MC20

Eosinophilic renal cell carcinoma

Intermed -1 (25%), -2 (52%), -7 (42%), -17

No detectable chromosomal abnormalities

Oncocytoma

Discrepant

No evidence of tumor

24


MC21

Oncocytic renal epithelial neoplasm

-1 (92%), -17 (37%), +7 (51%)

-1,+7, +9p, -9q

Oncocytoma (novel)

SNP diagnostic

No evidence of tumor

20


MC22

Renal cell carcinoma, unclassified

-1 (45%), 12 (37%), -17 (50%); intermed -7 (22%)

+7, +16

Papillary RCC

SNP diagnostic

No evidence of tumor

20


MC23

Eosinophilic renal cell carcinoma

-1 (49%), -2 (53%), -7 (49%), and -17 (74%)

No detectable chromosomal abnormalities

Oncocytoma

Discrepant

No evidence of tumor

22


MC24

Papillary renal cell carcinoma, type 2

-1 (48%), intermed -2 (23%), -7 (26%)

+7, +12, +17

Papillary RCC

Confirms

No evidence of tumor

27


MC26

Renal clear cell carcinoma

-2 intermed (23%). +7 (52%), -17 (43%)

-3p, unable to interpret other changes

Clear Cell RCC

Confirms

No evidence of tumor

1


MC28

Renal oncocytoma

-1 (37%), -2 (38%), -7 (30%), and -17 (55%)

No detectable chromosomal abnormalities

Oncocytoma

Confirms

No evidence of tumor

68


MC29

Papillary renal cell carcinoma, type II

-2 intermediate (20%),+7 (30%), +7+7 (18%)

+7, +16q (high normal contamination)

Papillary RCC

Confirms

No evidence of tumor

16


MC30

Renal oncocytoma

1 -(41%), 2 failed, -7(34%), -17(65%)

No detectable chromosomal abnormalities

Oncocytoma

Confirms

No evidence of tumor

71


MC31

Renal epithelial oncocytic neoplasm with features of an oncocytoma

-1 (67%), -2 (63%), -7 (42%), and -17 (40%)

No detectable chromosomal abnormalities

Oncocytoma

Confirms

No evidence of tumor

19


*Array Results vs. Final Diagnosis field summarizes the potential impact on diagnosis had the SNP array karyotype been available (confirms = virtual karyotype confirms the favored diagnosis; SNP diagnostic = the virtual karyotype could classify the tumor based on the pattern of genetic lesions while morphology with IHC and FISH could not; novel = new pattern seen on virtual karyotype and ambiguous morphology; discrepant = virtual karyotype diagnosis and morphologic diagnosis are discrepant).

Hagenkord et al. Diagnostic Pathology 2008 3:44   doi:10.1186/1746-1596-3-44

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