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Table 1 Genes under significant selection

From: Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome

Gene name

dN/dS

Q value

AP2S1

0.043

0.0107

BCL2L12 a

0.093

0.0001

RALBP1

0.121

0.0738

CLDN9

0.126

0.0625

GTSF1L b

0.178

0.0501

ZDHHC3

0.255

0.0625

DECR1

0.286

0.0341

HLA-DOA

0.291

0.0581

TMEM214

0.328

0.0408

GRID2IP a

0.331

0.0107

DAGLB

0.338

0.0241

GFRA3

0.351

0.0532

TERT

0.368

0.0007

KRI1

0.372

0.0408

ZBTB7C

0.379

0.0073

NPSR1

0.404

0.0241

AP1B1

0.41

0.0387

WISP1

0.421

0.0408

MCM2

0.434

0.0581

XKR6

0.471

0.0802

CYFIP1

0.475

0.0317

TYK2

0.521

0.0802

EPPK1

0.591

0.0073

CACNA1S

0.625

0.0632

TECTA b

0.626

0.0209

FGFR2

2.36

0.0802

ERBB3

2.523

0.0428

KEAP1

2.701

0.048

CTNNB1

3.344

0

SMAD4

3.976

0.0387

PTEN

4.756

0

FBXW7

5.577

0

HRAS

5.636

0.0802

PIK3CA

5.928

0

SPOP

6.89

0.0016

BRAF

9.782

0

TP53

10.304

0

IDH1

21.589

0

KRAS

25.681

0

  1. Genes with dN/dS < 1 are under negative selection
  2. aGenes with signals of negative selection potentially influenced by germline variants or positive selection on silent mutations: GRID2IP has 17 synonymous somatic mutations having an EXAC allele frequency > 0.001, BCL2L12 has a silent mutation cluster.
  3. bNot significant after removing non-diploid regions
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Genome Biology

ISSN: 1474-760X

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