Renal Table: Recurrent Genomic Alterations Detected by Chromosomal Microarray

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Table 1 - Recurrent Genomic Alterations in AML Detected by Chromosomal Microarray (Literature Review). This is a comprehensive list of CNAs and CN-LOH detectable by CMA testing with strong clinical significance in major types of renal cell neoplasia. Table derived from Liu et al., 2020 [PMID: 32434132] with permission from Cancer Genetics.

WHO Classification
Subtype Clear Cell RCC Papillary RCC

Type 1

Papillary RCC

Type 2

(heterogeneous group)

MiTF-Translocation RCC Chromophobe RCC Oncocytoma
Percentage 70-75% 15-20% 15-20% 1-5% 5% 5%
Origin Proximal    Tubules Collecting   Ducts
Copy Number Alterations [level of evidencea; clinical significanceb]
Whole genome Mostly gains Mostly losses No CNAs (~50%) [1; R]
chr1 1p- (10%) [2; R] 1p- (25%) [2; R] 1p- (30%) [3; R] -1 (90%) [1; D]c -1/1p- soly (50%) [1; R]
chr2 +2 (18%) [2; R] -2 (80%) [1; D]c
chr3 -3/3p- (VHL, KDM6A,

KDM5C, SETD2, PBRM1)

(90%) [1; D]

+3 (40%) [2; R] 3p-/cnLOH(3p) (21%) [2; R], 3p+ (12%) [3; R], 3q+ (21%) [3; R] -3 (25%) [3; R]
chr4 4p- (10%) [2; R] -4 (21%) [3; R] +4 (10%) [3; R]
chr5 5p+ (24%) [2; R],

5q+ (SQSTM1) (40-60%) [2; R]

5q+/+5 (20%) [2; R] -5 (25%) [3; R]
chr6 6q- (20%) [2; R] -6 (17%) [3; R] 6p21 (TFEB) amp [2; D, P] -6 (90%) [1; D]c
chr7 +7 (25%) [2; R] +7/+7,+7 (84%) [1; D]c +7 (25%) [1; D] +7 (30%) [3; R]
chr8 8p- (25%) [2; R] +8 (MYC) (10-33%) [3; R] -8 (15%) [3; R]c
chr9 9p- (20%) [1; P]

9q- (20%) [2; R]

9p- (19%) [2; R],

9q- (17%) [3; R]

9p- (30%) [3; R] -9 (35%) [3; R]
chr10 10q- (10%) [2; R] 10q- (17%) [3; R] -10 (90%) [1; D]c
chr11 11q- (19%) [3; R] -11 (10%) [3; R]
chr12 +12 (15%) [2; R] +12 (52%) [2; R] +12 (15%) [3; R] +12 (35%) [3; R]
chr13 +13 (13%) [2; R] -13 (20%) [3; R] -13 (85%) [1; D]c
chr14 14q- (HIF1A) (40%) [1; P] -14 (28%) [2; R] -14 (10%) [2; R]
chr15 -15 (15%) [3; R] -15 (15%) [3; R]
chr16 16p+ (12%) [2; R],

16q+ (10%) [2; R]

+16 (55%) [2; R] 16p+ (40%) [2; R],

16q+ (35%) [2; R]

chr17 +17 (84%) [1; D] c 17p- (8%) [3; R],

+17/17q+ (50%) [1; D]

17p- (20%) [3; R],

17q+ (40%) [3; R]

-17 (90%) [1; D]c
chr18 -18 (10%) [2; R] -18 (26%) [2; R] -18 (15%) [3; R]
chr19
chr20 +20 (13%) [2; R] +20 (40%) [2; R]
chr21 -21 (19%) [3; R] -21 (70%) [1; D]c -21 (15%) [3; R]
chr22 -22 (40%) [2; R]
X -X (10%) [3;R]
Y -Y (40%) [1; R with -1]c
Rearrangements [level of evidence; clinical significance]
TERT promoter (5p15) (<10%) [3; R] TFE3 (Xp11), TFEB (6p21) (100%) [1; D, P] TERT promoter (5p15) (12%) [3; R] CCND1 (11q13) (40%) [2; D]
Mutations (SNVs, Indels) [level of evidence; clinical significance]
Mutated

in >20%

PBRM1 [2; R], VHL (also promoter methylation) [1; D] TP53 [2; R]
Mutated

in 10-20%

BAP1 [1; P], SETD2 [2; R] MET [1; D]
Mutated

in 5-10%

KDM5C, MTOR, PTEN, TP53 [2; R] CDKN2A (also promoter hypermethylation) [2; P], MET [1; D] PTEN [2; R]
Mutated

in 2-5%

ARID1A, CDKN2A, KDMT2C/KDMT2D, LRP1B, PIK3CA, PTEN, STAG2, TCEB1, TERT CDKN2A/CDKN2B, KDM6A, MLL3, NF2, NFE2L2, SMARCB1, TERT BAP1, FAT1, KDM6A, NF2, NFE2L2, PBRM1, SETD2, STAG2, TERT, TP53 ARID1A, FAAH2, FAT1/FAT4, FLT4, MICALCL, NIN, PDHB, PDXDC1, TSC1/TSC2, ZNF765 ERCC2, C2CD4C
Mitochondrial  DNA MT-ND5 [3,D] MT-COX1, MT-COX2, MT-COX3, MT-ND5, MT-CYTB [2,D]
Germline susceptibility
Germline susceptibility § mainly VHL (von Hippel-Lindau Syndrome)

§ PTEN (Cowden Syndrome)

§ FLCN (Birt-Hogg-Dube syndrome)

§ TSC1 and TSC2 (tuberous sclerosis)

§ SDHB (most common), SDHC (less common), SDHA (rare), SDHD (rare) (succinate dehydrogenase deficient RCC)

§ MET (Hereditary papillary RCC) § FH (Hereditary leiomyomatosis and RCC) FCLN (Birt-Hogg-Dube syndrome) FCLN (Birt-Hogg-Dube syndrome)
References [9[1], 14[2], 17[3], 24[4], 27[5], 29[6], 32[7], 35[8], 49[9], 156-168[10][11][12][13][14][15][16][17][18][19][20][21][22]] [10[23], 42[24], 67-71[25][26][27][28][29], 73[30], 74[31], 98[32], 169-174[33][34][35][36][37][38]] [10[1], 121[39], 122[40], 124[41], 125[42], 175[43]] [11[44], 12[45], 103[46], 105[47], 106[48], 108[49], 109[50], 129[51], 137[52], 176[53], 177[54]] [12[45], 76[55], 102[56], 103[46], 105[47], 129[51], 132[57], 135-137[58][59][52], 140[60], 178-180[61][62][63]]

Note: a level of evidence (ranges from level 1 to 3 as specified in the methods). Level 1, established clinical significance and present in current WHO classification and/or professional practice guidelines such as NCCN, ASCO, CAP guidelines or FDA approval; Level 2, recurrent clinical significance based on large studies with outcomes; and Level 3, recurrent but uncertain clinical significance based on smaller studies and multiple case reports.

          b clinical significance, D-diagnosis, P-prognosis, R-recurrence

          c alterations in combination

Reference

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