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Table 1 The 21 best candidate genes that are MYCN-dependent and harbor recurrent, verified missense variants in HR-NB

From: Incorporating genomic, transcriptomic and clinical data: a prognostic and stem cell-like MYC and PRC imbalance in high-risk neuroblastoma

Hugo Symbol MYCN-associated expression Case USI Chromosome Start_Position Variant Classification Mycn statues Verification Method
AHCTF1 MA-hi TARGET-30-PAPNEP 1 247,063,482 Missense amp  
  TARGET-30-PASAZJ 1 247,014,426 Missense non-amp (2)
ALK MA-hi N130 T 2 29,286,167 Missense amp (1)
  N160 T 2 29,286,167 Missense gain (1)
  N744 T 2 29,286,167 Missense non-amp (1)
  N198 T 2 29,297,200 Missense non-amp (1)
  TARGET-30-PAKXDZ 2 29,445,213 Missense amp (3)
  TARGET-30-PANRVJ 2 29,443,697 Missense non-amp (4)
  TARGET-30-PARKNP 2 29,443,697 Missense non-amp (4)
  TARGET-30-PARLTG 2 29,443,696 Missense non-amp (4)
  TARGET-30-PARZIP 2 29,443,696 Missense non-amp (4)
  TARGET-30-PAPRPR 2 29,443,695 Missense amp (4)
  TARGET-30-PASVRU 2 29,443,695 Missense amp (4)
  TARGET-30-PATFXV 2 29,443,695 Missense amp (4)
  TARGET-30-PALAKE 2 29,443,695 Missense amp (3)
  TARGET-30-PANZVU 2 29,443,695 Missense non-amp (3)
  TARGET-30-PATFCY 2 29,436,875 Missense non-amp (4)
  TARGET-30-PAINLN 2 29,436,860 Missense non-amp (3)
  TARGET-30-PASKFV 2 29,432,664 Missense amp (4)
  TARGET-30-PANWRR 2 29,432,664 Missense non-amp (4)
  TARGET-30-PANXJL 2 29,432,664 Missense non-amp (4)
  TARGET-30-PAPTFZ 2 29,432,664 Missense amp (4)
  TARGET-30-PAPTLV 2 29,432,664 Missense amp (4)
  TARGET-30-PARURB 2 29,432,664 Missense non-amp (4)
  TARGET-30-PALNLU 2 29,432,664 Missense non-amp (3)
  TARGET-30-PANBCI 2 29,432,664 Missense amp (3)
  TARGET-30-PASAZJ 2 29,432,664 Missense non-amp (2) (4)
  TARGET-30-PAREGK 2 29,443,695 Missense non-amp (2)(5)
ATM MA-hi TARGET-30-PANYGR 11 108,196,934 Silent non-amp  
  TARGET-30-PANRHJ 11 108,200,975 Missense non-amp  
  TARGET-30-PANRRW 11 108,196,798 Missense non-amp (2)
FANCM MA-hi TARGET-30-PASXRG 14 45,646,146 Missense amp (4)
  TARGET-30-PARHUX 14 45,657,091 Splice_Site amp (4)
  TARGET-30-PARETE 14 45,658,176 Nonsense amp (4)
  N492 T 14   Mut. Splice Junction non-amp  
MRPS27 MA-hi TARGET-30-PAPSKM 5 71,519,665 Missense non-amp (2)(5)
  TARGET-30-PAPSKM 5 71,522,027 Splice_Site_GWAS SNP non-amp (2)(5)
MSH2 MA-hi TARGET-30-PAITCI 2 47,641,416 Silent non-amp  
  TARGET-30-PARKNP 2 47,693,815 Frame_Shift_Del non-amp (4)
  N538 T 2 2,367,537 Protein Fusion amp  
MYCN MA-hi TARGET-30-PAPLSD 2 16,082,317 Missense non-amp (4)
  TARGET-30-PARCRR 2 16,082,317 Missense non-amp (4)
  TARGET-30-PARVNT 2 16,082,317 Missense non-amp (4)
  TARGET-30-PASLGS 2 16,082,317 Missense non-amp (2)(3)(5)
  NB-1744-Tumor 19 19,337,844 Missense   (4)
  N619 T 2 16,003,271 Missense amp (1)
NCAN MA-hi TARGET-30-PANIPC 19 19,337,844 Missense amp (4)
  TARGET-30-PAPKXS 19 19,338,389 Missense non-amp (4)
  TARGET-30-PANLET 19 19,359,524 Missense non-amp (4)
STAG1 MA-hi TARGET-30-PAIPGU 3 136,117,607 Missense non-amp  
  TARGET-30-PARDCK 3 136,078,044 Missense non-amp  
  TARGET-30-PAPZFW 3 136,057,265 Frame_Shift_Del non-amp (4)
BARD1 MA-hi TARGET-30-PATGWT 2 215,595,215 Nonsense; 1p-;17q+ amp (3)
  TARGET-30-PAHYWC 2 215,657,051 Nonsense; 9p-; 10q-;17q+ amp (3)
  GWAS 2 215,672,546 GWAS SNP   (6)
  GWAS 2 215,635,794 GWAS SNP   (6)
ARID1A MN-hi TARGET-30-PALNLU 1 27,099,000 Missense non-amp (3)
  TARGET-30-PALXHW 1 27,106,214 Missense non-amp (3)
  N554 T 1 26,970,220 DEL amp (1)
CACNB3 MN-hi TARGET-30-PAMDAL 12 49,220,231 Missense amp (4)
  N608 T 12 47,505,015 Missense amp (1)
IL16 MN-hi TARGET-30-PAIMDT 15 81,561,966 Missense non-amp (3)
  N170 T 15 79,385,873 Missense non-amp (1)
INPP5D MN-hi TARGET-30-PANUIF 2 234,070,424 Missense non-amp (4)
  TARGET-30-PANRVJ 2 234,098,527 Missense non-amp (4)
LRRTM4 MN-hi TARGET-30-PATEPF 2 77,746,658 Frame_Shift_Ins non-amp (4)
  N717 T 2 77,600,317 GWAS SNP amp (1)
MLL5 MN-hi TARGET-30-PARBLH 7 104,748,301 Missense non-amp  
  TARGET-30-PANYGR 7 104,753,479 Missense non-amp (2)
  N198 T 7 104,437,581–104,447,802 Deletion non-amp  
NCAM1 MN-hi TARGET-30-PAPZFW 11 113,130,966 Silent non-amp (4)
  TARGET-30-PASGUT 11 113,077,981 Splice_Site non-amp (4)
NRAS MN-hi TARGET-30-PANBSP 1 115,258,745 Missense non-amp (4)
  TARGET-30-PAPTMM 1 115,256,530 Missense amp (2)(5)
SYNRG MN-hi TARGET-30-PARDIW 17 35,930,941 Missense non-amp  
  TARGET-30-PASAZJ 17 35,956,340 Missense non-amp (2)(5)
TLN2 MN-hi TARGET-30-PASRFS 15 63,029,117 Silent non-amp  
  TARGET-30-PARNNG 15 63,030,490 Missense non-amp  
  TARGET-30-PARIRD 15 62,942,372 Missense amp (2)(5)
LMO1 MN-hi GWAS 10 8,252,853 GWAS SNP   (6)
  GWAS 10 8,238,639 GWAS SNP   (6)
  1. The information was collected from the Table S3 of Pugh 2013 Nature paper and the Tables S1, S3, S6 of Molenaar 2012 Nature paper. All patients are with high-risk neuroblastoma (TARGET_NBL_clinicalCovariates20120702.txt)
  2. Validation Method: (1) linkage disequilibrium analysis; (2) PCR/HiSeq; (3) Sequenom; (4) PCR/MiSeq; (5) PCR/Sanger; (6) GWAS