Cytognomix has designed and developed a unique type of reagents for targeted hybridization capture of breast cancer genes. These capture reagent have maximal coverage of complete unique gene sequences, covering exons, but also promoter, intronic, and downstream flanking genomic regions. This extensive coverage of regulatory regions is intended to produce companion data for our patented methods for interpreting non-coding variants of unknown significance. Besides single copy sequences, divergent interspersed repetitive element probes extend the genomic coverage in these genes. This targeting results in the most comprehensive coverage available (Dorman et al. Nucleic Acids Res., 2013).
Our hybridization capture array products can be used for mutation detection in hereditary cancer and pharmacogenetic applications and are ready-to-ship:
A. Inherited breast and ovarian cancer complete gene and flanking regions (Caminsky et al. submitted; Mucaki et al. submitted):
Version 1: BRCA1, BRCA2, ATM, CDH1, CHEK2, PALB2, and TP53.
Version 2: ATM, BARD1, BRCA1, BRCA2, CDH1, CHEK2, EPCAM, MLH1, MRE11A, MSH2, MSH6, MUTYH, NBN, PALB2, PMS2, PTEN, RAD51B, STK11, TP53, and XRCC2
B. Chemotherapy resistance (combined paclitaxel + gemcitabine mutation targets; Dorman et al. 2015):
Paclitaxel response: ABCB1, ABCB11, ABCC1, ABCC10, BAD, BBC3, BCAP29, BCL2, BCL2L1, BIRC5, BMF, CNGA3, CSAG2, CYP2C8, CYP3A4, FGF2, FN1, GBP1, MAP2, MAP4, MAPT, NFKB2, NR1I2, OPRK1, SLCO1B3, TLR6, TMEM243, TUBB1, TUBB4A, TUBB4B, TWIST1
Gemcitabine response: ABCB1, ABCC10, AK1, CDA, CMPK1, CTPS1, DCK, DCTD, NME1, NT5C, RRM1, RRM2, RRM2B, SLC28A1, SLC28A3, SLC29A1, SLC29A2, TYMS
C. A subscription to our MutationForecaster system provides genome browser access to our genome-wide custom probe designs through the cytogenetic Visual Analytics Decision Support Tool. This tool displays the locations of oligonucleotide products used in hybridization enrichment for Next generation sequencing.
1) Dorman et al. Expanding probe repertoire and improving reproducibility in human genomic hybridization Nucleic Acids Research 2013; doi: 10.1093/nar/gkt048 This paper has been cited:
“Microarray-based comparative genomic hybridization (aCGH) is widely used in biomedical applications and life sciences research to detect and analyze structural variation in genomes, and novel applications are constantly developed (Dorman et al. 2013)…. Jonker et al. Nucl. Acids Res. (2014)“
3) Mucaki et al. A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer. Preprint at BioRxiv. http://dx.doi.org/10.1101/031419 (submitted for publication)
4) Caminsky et al. Prioritizing variants in complete Hereditary Breast and Ovarian Cancer (HBOC) genes in patients lacking known BRCA mutations. Preprint at BioRxiv. http://dx.doi.org/10.1101/039206 (submitted for publication).
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