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Table 1 Predicted protein coding somatic changes within the initial and the drug resistant recurrent tumor

From: Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors

Tumor

Chr.

Ensembl gene ID

Ensembl display

HUGO ID

Chr. position

Ref.

Obs.

Het.

Protein position

Ref. amino acid

Alt. amino acid

Description

Initial

6

ENSG00000197062

ZNF187-201

12978

28352058

G

T

K

62

G

C

Zinc finger protein 187 (Zinc finger and SCAN domain-containing protein 26) (Protein SRE-ZBP)

Initial

8

ENSG00000169946

ZFPM2-202

16700

106884238

A

G

R

785

K

E

Zinc finger protein ZFPM2 (Zinc finger protein multitype 2) (Friend of GATA protein 2) (FOG-2) (hFOG-2)

Initial

13

ENSG00000139687

RB1-002

9884

47832247

T

A

W

234

L

*

Retinoblastoma-associated protein (pRb) (Rb) (pp110) (p105-Rb)

Initial

17

ENSG00000141510

TP53-202

11998

7518231

C

A

M

259

D

Y

Cellular tumor antigen p53 (Tumor suppressor p53) (Phosphoprotein p53) (Antigen NY-CO-13)

Recurrence

1

ENSG00000146463

ZMYM4-001

13055

35608585

G

C

S

317

Q

H

Zinc finger MYM-type protein 4 (Zinc finger protein 262)

Recurrence

2

ENSG00000118997

DNAH7-201

18661

196431742

C

G

S

2590

V

L

Dynein heavy chain 7, axonemal (Axonemal beta dynein heavy chain 7) (Ciliary dynein heavy chain 7) (Dynein heavy chain-like protein 2) (HDHC2)

Recurrence

4

ENSG00000156234

CXCL13-001

10639

78747983

G

A

R

56

R

H

C-X-C motif chemokine 13 Precursor (Small-inducible cytokine B13) (B lymphocyte chemoattractant) (CXC chemokine BLC) (B cell-attracting chemokine 1) (BCA-1) (ANGIE)

Recurrence

6

ENSG00000204228

HSD17B8-001

3554

33281235

G

A

R

141

A

T

Estradiol 17-beta-dehydrogenase 8 (EC 1.1.1.62) (Testosterone 17-beta-dehydrogenase 8) (EC 1.1.1.63) (17-beta-hydroxysteroid dehydrogenase 8) (17-beta-HSD 8) (Protein Ke6) (Ke-6)

Recurrence

7

ENSG00000186472

PCLO-201

13406

82419723

T

C

Y

2759

T

A

Protein piccolo (Aczonin)

Recurrence

11

ENSG00000152578

GRIA4-201

4574

105355581

C

T

Y

872

R

C

Glutamate receptor 4 Precursor (GluR-4) (GluR4) (GluR-D) (Glutamate receptor ionotropic, AMPA 4) (AMPA-selective glutamate receptor 4)

Recurrence

14

ENSG00000165762

OR4K2-201

14728

19414855

C

T

Y

197

L

F

Olfactory receptor 4K2 (Olfactory receptor OR14-15)

Recurrence

14

ENSG00000054654

SYNE2-206

17084

63500386

C

G

S

302

A

G

Nesprin-2 (Nuclear envelope spectrin repeat protein 2) (Synaptic nuclear envelope protein 2) (Syne-2) (Nucleus and actin connecting element protein) (Protein NUANCE)

Recurrence

18

ENSG00000173482

PTPRM-202

9675

8333477

G

A

R

929

A

T

Receptor-type tyrosine-protein phosphatase mu Precursor (Protein-tyrosine phosphatase mu) (R-PTP-mu) (EC 3.1.3.48)

  1. Validated non-synonymous single nucleotide variations (SNVs) predicted by high-throughput sequencing are listed with the corresponding chromosome (CHr.), Ensembl gene ID, the HUGO ID, chromosomal position, the identity of the base at this location in the reference genome (Ref.), the observed base that does not match the reference (Obs.), and the IUPAC code at the heterogeneous position (Het.), the position in the protein where the amino acid changed as a result of the SNV, the reference amino acid, the altered amino acid, and the Ensembl description for this gene. Those marked as 'Initial' (first four SNVs) were identified in the primary tumor and were validated using PCR and Sanger sequencing on germline and tumor genomic DNA. Those marked as 'Recurrence' (remaining nine SNVs) were identified in the post-treatment secondary tumor and were validated by Illumina sequencing. SNVs in the initial tumor were also identified and validated in the recurrent tumor.
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Genome Biology

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