Table 3.
List of genes analyzed by targeted next-generation sequencing
| Abbreviation | Gene name (alternative denominations) |
|---|---|
| AIP | Aryl hydrocarbon receptor interacting protein |
| ALK | Anaplastic lymphoma kinase |
| APC | Adenomatous polyposis coli |
| APEX1 | APEX nuclease (multifunctional DNA repair enzyme) 1 |
| ATM | Ataxia telangiectasia mutated |
| ATMIN | ATM interactor |
| ATR | Ataxia telangiectasia and Rad3 related |
| ATRIP | ATR interacting protein |
| AURKA | Aurora kinase A |
| AXIN1 | Axin 1 |
| BABAM1 | BRISC and BRCA1 A complex member 1 |
| BAP1 | BRCA1-associated protein-1 (ubiquitin carboxy-terminal hydrolase) |
| BARD1 | BRCA1-associated RING domain 1 |
| BLM | Bloom syndrome, RecQ helicase-like |
| BMPR1A | Bone morphogenetic protein receptor, type IA |
| BRAP | BRCA1-associated protein |
| BRCA1 | Breast cancer 1, early onset |
| BRCA2 | Breast cancer 2, early onset |
| BRCC3 | BRCA1/BRCA2-containing complex, subunit 3 |
| BRE | Brain and reproductive organ-expressed (TNFRSF1A modulator) |
| BRIP1 | BRCA1 interacting protein C-terminal helicase 1 |
| BUB1B | Budding uninhibited by benzimidazoles 1 homolog beta (yeast) |
| C11orf30 | Chromosome 11 open reading frame 30 (EMSY) |
| C19orf40 | Chromosome 19 open reading frame 40 (FAAP24) |
| CASP8 | Caspase 8, apoptosis-related cysteine peptidase |
| CCND1 | Cyclin D1 |
| CDC73 | Cell division cycle 73, Paf1/RNA polymerase II complex component, homolog (Saccharomyces cerevisiae) |
| CDH1 | Cadherin 1, type 1, E-cadherin (epithelial) |
| CDK4 | Cyclin-dependent kinase 4 |
| CDKN1B | Cyclin-dependent kinase inhibitor 1B (p27, Kip1) |
| CDKN1C | Cyclin-dependent kinase inhibitor 1C (p57, Kip2) |
| CDKN2A | Cyclin-dependent kinase inhibitor 2A |
| CEBPA | CCAAT/enhancer binding protein (C/EBP), alpha |
| CEP57 | Centrosomal protein 57 kDa |
| CLSPN | Claspin |
| CSNK1D | Casein kinase 1, delta |
| CSNK1E | Casein kinase 1, epsilon |
| CWF19L2 | CWF19-like 2, cell cycle control (Schizosaccharomyces pombe) |
| CYLD | Cylindromatosis (turban tumor syndrome) |
| DCLRE1C | DNA cross-link repair 1C |
| DDB2 | Damage-specific DNA binding protein 2, 48 kDa |
| DHFR | Dihydrofolate reductase |
| DICER1 | Dicer 1, ribonuclease type III |
| DMC1 | DMC1 dosage suppressor of mck1 homolog, meiosis-specific homologous recombination (yeast) |
| DNAJC21 | DnaJ (Hsp40) homolog, subfamily C, member 21 |
| DPYD | Dihydropyrimidine dehydrogenase |
| EGFR | Epidermal growth factor receptor |
| EPCAM | Epithelial cell adhesion molecule |
| EPHX1 | Epoxide hydrolase 1, microsomal (xenobiotic) |
| ERCC1 | Excision repair cross-complementing rodent repair deficiency, complementation group 1 |
| ERCC2 | Excision repair cross-complementing rodent repair deficiency, complementation group 2 |
| ERCC3 | Excision repair cross-complementing rodent repair deficiency, complementation group 3 |
| ERCC4 | Excision repair cross-complementing rodent repair deficiency, complementation group 4 |
| ERCC5 | Excision repair cross-complementing rodent repair deficiency, complementation group 5 |
| ERCC6 | Excision repair cross-complementing rodent repair deficiency, complementation group 6 |
| ESR1 | Estrogen receptor 1 |
| ESR2 | Estrogen receptor 2 (ER beta) |
| EXO1 | Exonuclease 1 |
| EXT1 | Exostosin 1 |
| EXT2 | Exostosin 2 |
| EYA2 | Eyes absent homolog 2 (Drosophila) |
| EZH2 | Enhancer of zeste homolog 2 (Drosophila) |
| FAM175A | Family with sequence similarity 175, member A |
| FAM175B | Family with sequence similarity 175, member B |
| FAN1 | FANCD2/FANCI-associated nuclease 1 |
| FANCA | Fanconi anemia, complementation group A |
| FANCB | Fanconi anemia, complementation group B |
| FANCC | Fanconi anemia, complementation group C |
| FANCD2 | Fanconi anemia, complementation group D2 |
| FANCE | Fanconi anemia, complementation group E |
| FANCF | Fanconi anemia, complementation group F |
| FANCG | Fanconi anemia, complementation group G |
| FANCI | Fanconi anemia, complementation group I |
| FANCL | Fanconi anemia, complementation group L |
| FANCM | Fanconi anemia, complementation group M |
| FBXW7 | F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase |
| FH | Fumarate hydratase |
| FLCN | Folliculin |
| GADD45A | Growth arrest and DNA-damage-inducible, alpha |
| GATA2 | GATA binding protein 2 |
| GPC3 | Glypican 3 |
| GRB7 | Growth factor receptor-bound protein 7 |
| HELQ | Helicase, POLQ-like |
| HNF1A | HNF1 homeobox A |
| HOXB13 | Homeobox B13 |
| HRAS | v-Ha-ras Harvey rat sarcoma viral oncogene homolog |
| HUS1 | HUS1 checkpoint homolog (S. pombe) |
| CHEK1 | Checkpoint kinase 1 |
| CHEK2 | Checkpoint kinase 2 |
| KAT5 | K(lysine) acetyltransferase 5 |
| KCNJ5 | Potassium inwardly rectifying channel, subfamily J, member 5 |
| KIT | V-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog |
| LIG1 | Ligase I, DNA, ATP-dependent |
| LIG3 | Ligase III, DNA, ATP-dependent |
| LIG4 | Ligase IV, DNA, ATP-dependent |
| LMO1 | LIM domain only 1 (rhombotin 1) |
| LRIG1 | Leucine-rich repeats and immunoglobulin-like domains 1 |
| MAX | MYC-associated factor X |
| MCPH1 | Microcephalin 1 |
| MDC1 | Mediator of DNA-damage checkpoint 1 |
| MDM2 | Mdm2, p53 E3 ubiquitin protein ligase homolog (mouse) |
| MDM4 | Mdm4 p53 binding protein homolog (mouse) |
| MEN1 | Multiple endocrine neoplasia I |
| MET | Met proto-oncogene (hepatocyte growth factor receptor) |
| MGMT | O-6-methylguanine-DNA methyltransferase |
| MLH1 | mutL homolog 1, colon cancer, nonpolyposis type 2 (Escherichia coli) |
| MLH3 | mutL homolog 3 (E. coli) |
| MMP8 | Matrix metallopeptidase 8 (neutrophil collagenase) |
| MPL | Myeloproliferative leukemia virus oncogene |
| MRE11A | MRE11 meiotic recombination 11 homolog A (S. cerevisiae) |
| MSH2 | mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli) |
| MSH3 | mutS homolog 3 (E. coli) |
| MSH5 | mutS homolog 5 (E. coli) |
| MSH6 | mutS homolog 6 (E. coli) |
| MSR1 | Macrophage scavenger receptor 1 |
| MUS81 | MUS81 endonuclease homolog (S. cerevisiae) |
| MUTYH | mutY homolog (E. coli) |
| NAT1 | N-acetyltransferase 1 (arylamine N-acetyltransferase) |
| NBN | Nibrin |
| NCAM1 | Neural cell adhesion molecule 1 |
| NELFB | Cofactor of BRCA1 |
| NF1 | Neurofibromin 1 |
| NF2 | Neurofibromin 2 (merlin) |
| NFKBIZ | Nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta |
| NHEJ1 | Nonhomologous end-joining factor 1 |
| NSD1 | Nuclear receptor binding SET domain protein 1 |
| OGG1 | 8-oxoguanine DNA glycosylase |
| PALB2 | Partner and localizer of BRCA2 |
| PARP1 | Poly (ADP-ribose) polymerase 1 |
| PCNA | Proliferating cell nuclear antigen |
| PHB | Prohibitin |
| PHOX2B | Paired-like homeobox 2b |
| PIK3CG | Phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma |
| PLA2G2A | Phospholipase A2, group IIA (platelets, synovial fluid) |
| PMS1 | PMS1 postmeiotic segregation increased 1 (S. cerevisiae) |
| POLB | Polymerase (DNA directed), beta |
| POLD1 | Polymerase (DNA directed), delta 1, catalytic subunit |
| POLE | Polymerase (DNA directed), epsilon, catalytic subunit |
| PPM1D | Protein phosphatase, Mg2+/Mn2+ dependent, 1D |
| PREX2 | Phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2 |
| PRF1 | Perforin 1 (pore forming protein) |
| PRKAR1A | Protein kinase, cAMP-dependent, regulatory, type I, alpha |
| PRKDC | Protein kinase, DNA-activated, catalytic polypeptide |
| PTEN | Phosphatase and tensin homolog |
| PTCH1 | Patched 1 |
| PTTG2 | Pituitary tumor-transforming 2 |
| RAD1 | RAD1 homolog (S. pombe) |
| RAD17 | RAD17 homolog (S. pombe) |
| RAD18 | RAD18 homolog (S. cerevisiae) |
| RAD23B | RAD23 homolog B (S. cerevisiae) |
| RAD50 | RAD50 homolog (S. cerevisiae) |
| RAD51 | RAD51 homolog (S. cerevisiae) |
| RAD51AP1 | RAD51 associated protein 1 |
| RAD51B | RAD51 homolog B (S. cerevisiae) |
| RAD51C | RAD51 homolog C (S. cerevisiae) |
| RAD51D | RAD51 homolog D (S. cerevisiae) |
| RAD52 | RAD52 homolog (S. cerevisiae) |
| RAD54B | RAD54 homolog B (S. cerevisiae) |
| RAD54L | RAD54-like (S. cerevisiae) |
| RAD9A | RAD9 homolog A (S. pombe) |
| RB1 | Retinoblastoma 1 |
| RBBP8 | Retinoblastoma binding protein 8 |
| RECQL | RecQ protein-like (DNA helicase Q1-like) |
| RECQL4 | RecQ protein-like 4 |
| RECQL5 | RecQ protein-like 5 |
| RET | Ret proto-oncogene |
| RFC1 | Replication factor C (activator 1) 1, 145 kDa |
| RFC2 | Replication factor C (activator 1) 2, 40 kDa |
| RFC4 | Replication factor C (activator 1) 4, 37 kDa |
| RHBDF2 | Rhomboid 5 homolog 2 (Drosophila) |
| RNF146 | Ring finger protein 146 |
| RNF168 | Ring finger protein 168, E3 ubiquitin protein ligase |
| RNF8 | Ring finger protein 8, E3 ubiquitin protein ligase |
| RPA1 | Replication protein A1, 70 kDa |
| RUNX1 | Runt-related transcription factor 1 |
| SDHAF2 | Succinate dehydrogenase complex assembly factor 2 |
| SDHB | Succinate dehydrogenase complex, subunit B, iron sulfur (Ip) |
| SETBP1 | SET binding protein 1 |
| SETX | Senataxin |
| SHPRH | SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase |
| SLX4 | SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae) |
| SMAD4 | SMAD family member 4 |
| SMARCA4 | SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily a, member 4 |
| SMARCB1 | SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily b, member 1 |
| SMARCE1 | SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily e, member 1 |
| STK11 | Serine/threonine kinase 11 |
| SUFU | Suppressor of fused homolog (Drosophila) |
| TCL1A | T-cell leukemia/lymphoma 1A |
| TELO2 | TEL2, telomere maintenance 2, homolog (S. cerevisiae) |
| TERF2 | Telomeric repeat binding factor 2 |
| TERT | Telomerase reverse transcriptase |
| TLR2 | Toll-like receptor 2 |
| TLR4 | Toll-like receptor 4 |
| TMEM127 | Transmembrane protein 127 |
| TOPBP1 | Topoisomerase (DNA) II binding protein 1 |
| TP53 | Tumor protein p53 |
| TP53BP1 | Tumor protein p53 binding protein 1 |
| TSC1 | Tuberous sclerosis 1 |
| TSC2 | Tuberous sclerosis 2 |
| TSHR | Thyroid stimulating hormone receptor |
| UBE2A | Ubiquitin-conjugating enzyme E2A |
| UBE2B | Ubiquitin-conjugating enzyme E2B |
| UBE2I | Ubiquitin-conjugating enzyme E2I |
| UBE2V2 | Ubiquitin-conjugating enzyme E2 variant 2 |
| UBE4B | Ubiquitination factor E4B |
| UIMC1 | Ubiquitin interaction motif containing 1 |
| VHL | Von Hippel–Lindau tumor suppressor, E3 ubiquitin protein ligase |
| WRN | Werner syndrome, RecQ helicase-like |
| WT1 | Wilms tumor 1 |
| XPA | Xeroderma pigmentosum, complementation group A |
| XPC | Xeroderma pigmentosum, complementation group C |
| XRCC1 | X-ray repair complementing defective repair in Chinese hamster cells 1 |
| XRCC2 | X-ray repair complementing defective repair in Chinese hamster cells 2 |
| XRCC3 | X-ray repair complementing defective repair in Chinese hamster cells 3 |
| XRCC4 | X-ray repair complementing defective repair in Chinese hamster cells 4 |
| XRCC5 | X-ray repair complementing defective repair in Chinese hamster cells 5 |
| XRCC6 | X-ray repair complementing defective repair in Chinese hamster cells 6 |
| ZNF350 | Zinc finger protein 350 |
| ZNF365 | Zinc finger protein 365 |