Genome-scale mutation interpretation software
The Shannon pipeline for splicing mutation analysis is the only genome-scale product on the market to comprehensively predict mRNA splicing mutations in exomes or complete genomes. This proprietary product finds mutations that no other software, public domain or commercial, detects. It is based on a proven technology backed up by more than 225 peer-reviewed publications, and thousands of users. A plug-in is available for the CLC Bio Genomics Workbench and Server.
Solution capture hybridization
Oligonucleotide pools covering unique sequences present in promoter, intragenic, and downstream regions have been designed for a series of genes. These reagents enable targeted enrichment of specific genes in any next generation, high throughput sequencing platform.The coverage using ab initio technology extends beyond products available from others, since Cytognomix covers both repeat-masked and divergent repetitive sequences with properties of unique sequences. This means that high multiplicity coverage is available for regions that were previously avoided – regions potentially containing mutations that would have been missed by other commercially available capture libraries.
Laboratory-validated SCFISH probes.
The applicability and precision of the SCFISH has been established for over twenty different chromosomal disorders, covered by over seventy different probes, and all currently available. This set includes probes for congenital syndromes and leukemias, for conditions such as Monosomy 1p36, Wolf-Hirschorn, Cri-du-Chat, Chronic Myelogenous Leukemia (CML), Acute Lymphoblastic Leukemia (ALL), Acute Myeloid Leukemia (AML), Prader-Willi & Angelman, Smith-Magenis Syndromes, and many others. A complete set of subtelomeric SCFISH probes has also been validated for detection of chromosome imbalances close to the termini of individual chromosomes.
The Cytognomix SC Genome Browser.
The Company’s SC Genome Browser contains design information on over 220,000 ab initio single-copy intervals for which SC FISH probes have been pre-designed or are being used for microarray content development. The probes can be selected by chromosomal location (band or genomic coordinate), by gene locus, and by disease or phenotype. Each probe is unique, and is representative of a single–copy interval, as assigned by the Company’s proprietary ab initio processes. Please visit the browser website or request an account for access to these products.
Microarray product designs for array comparative genomic hybridization.
Array CGH is used to identify chromosome abnormalities by genome-wide assessment of sequence copy number. Fundamental questions remain about data quality, evident by inter-platform comparisons monitored by the US FDA. Coefficients of variation remain high between platforms. We have shown that noise in genomic hybridization is related to contaminating SC sequences present in repeat-enriched (C0t-1 DNA) used to block repetitive sequences, and repetitive sequences in local context to single copy probes on those arrays. Systematic noise in microarray data can be reduced with ab initio SC designs, eliminate the requirement for C0t-1 DNA and obviate its effects.
Cytognomix’s founders previously invented and carried out studies based on repeat-masked approaches* for SCFISH probe design. In most instances, these probes perform as expected, however, we have found that only ab initio technology can assure true genome-wide SC designs.