Solution capture pools for targeted deep sequencing

Jun 26, 2012   //   by Peter Rogan   //   product, products, Targeted enrichment  //  No Comments

BRCA1Cytognomix 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.

References: 

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)“

2)  Dorman et al.  Genomic signatures for paclitaxel and gemcitabine resistance in breast cancer derived by machine learning. Mol. Onc. 2015.  http://dx.doi.org/10.1016/j.molonc.2015.07.006

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).

 

Contact:  info@scprobe.info, 519-661-4255

 

 

 

 

Capture reagents are based on our patented ab initio technology (US Patents 7,734,424,  8,209,129, and 8,407,013)

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