title: In silico SNP analysis of the breast cancer antigen NY-BR-1.
abstract: Breast cancer is one of the most common malignancies with increasing incidences every year and a leading cause of death among women. Although early stage breast cancer can be effectively treated, there are limited numbers of treatment options available for patients with advanced and metastatic disease. The novel breast cancer associated antigen NY-BR-1 was identified by SEREX analysis and is expressed in the majority (>70%) of breast tumors as well as metastases, in normal breast tissue, in testis and occasionally in prostate tissue. The biological function and regulation of NY-BR-1 is up to date unknown.
  
  
  
  We performed an in silico analysis on the genetic variations of the NY-BR-1 gene using data available in public SNP databases and the tools SIFT, Polyphen and Provean to find possible functional SNPs. Additionally, we considered the allele frequency of the found damaging SNPs and also analyzed data from an in-house sequencing project of 55 breast cancer samples for recurring SNPs, recorded in dbSNP.
  
  
  
  Over 2800 SNPs are recorded in the dbSNP and NHLBI ESP databases for the NY-BR-1 gene. Of these, 65 (2.07%) are synonymous SNPs, 191 (6.09%) are non-synoymous SNPs, and 2430 (77.48%) are noncoding intronic SNPs. As a result, 69 non-synoymous SNPs were predicted to be damaging by at least two, and 16 SNPs were predicted as damaging by all three of the used tools. The SNPs rs200639888, rs367841401 and rs377750885 were categorized as highly damaging by all three tools. Eight damaging SNPs are located in the ankyrin repeat domain (ANK), a domain known for its frequent involvement in protein-protein interactions. No distinctive features could be observed in the allele frequency of the analyzed SNPs.
  
  
  
  Considering these results we expect to gain more insights into the variations of the NY-BR-1 gene and their possible impact on giving rise to splice variants and therefore influence the function of NY-BR-1 in healthy tissue as well as in breast cancer.
authors.affiliation: Clinical Cooperation Unit "Applied Tumor Immunity", National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany.|, Im Neuenheimer Feld 460, 69120, Heidelberg, Germany.
authors.forename: Zeynep
authors.initials: Z
authors.lastname: Kosaloglu
authors.affiliation: Department of Medical Oncology, National Center for Tumor Diseases (NCT) and University Hospital Heidelberg, Heidelberg, Germany.|, Im Neuenheimer Feld 460, 69120, Heidelberg, Germany.
authors.forename: Julia
authors.initials: J
authors.lastname: Bitzer
authors.affiliation: Department of Medical Oncology, National Center for Tumor Diseases (NCT) and University Hospital Heidelberg, Heidelberg, Germany.|, Im Neuenheimer Feld 460, 69120, Heidelberg, Germany.
authors.forename: Niels
authors.initials: N
authors.lastname: Halama
authors.affiliation: Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.|, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.
authors.forename: Zhiqin
authors.initials: Z
authors.lastname: Huang
authors.affiliation: Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.|, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.
authors.forename: Marc
authors.initials: M
authors.lastname: Zapatka
authors.affiliation: Department of Obstetrics and Gynecology, National Center for Tumor Diseases (NCT) and University Hospital Heidelberg, Heidelberg, Germany.|, Im Neuenheimer Feld 460, 69120, Heidelberg, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Schneeweiss
authors.affiliation: Clinical Cooperation Unit "Applied Tumor Immunity", National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany.|Department of Medical Oncology, National Center for Tumor Diseases (NCT) and University Hospital Heidelberg, Heidelberg, Germany.|, Im Neuenheimer Feld 460, 69120, Heidelberg, Germany.
authors.forename: Dirk
authors.initials: D
authors.lastname: Jäger
authors.affiliation: Department of Medical Oncology, National Center for Tumor Diseases (NCT) and University Hospital Heidelberg, Heidelberg, Germany. Inka.Zoernig@nct-heidelberg.de.|, Im Neuenheimer Feld 460, 69120, Heidelberg, Germany. Inka.Zoernig@nct-heidelberg.de.
authors.forename: Inka
authors.initials: I
authors.lastname: Zörnig
mesh_terms: D000951:Antigens, Neoplasm / Q000235:genetics*; D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology; D015331:Cohort Studies; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D057225:Data Mining / Q000379:methods; D030541:Databases, Genetic; D005260:Female; D006801:Humans; D020641:Polymorphism, Single Nucleotide
chemical_list: C509866:ANKRD30A protein, human; D000951:Antigens, Neoplasm
keywords: Antigen; Breast cancer; In silico; NY-BR-1; SNPs