Polymorphism is everywhere – more than meets the eye. Use it. Ask questions. Get answers, often, quite fast.
If you’re ready to transition from marker discovery to screening key mutations in 1000’s of samples, rapidly and at low cost – we can help.
No SNPs? No problem. We’ve sequenced over 100 organisms and truly enjoy the discovery phase.
Our specialty is targeted-sequencing (also known as amplicon sequencing) using a novel pre-sequencing technology called MonsterPlex.
MonsterPlex targets (e.g. 60 to 190bp amplicons) are amplified in multiplex PCR reactions (e.g. up to 800 in a single PCR reaction). A unique 12bp barcode is added during the amplification and all the barcoded amplicons are pooled for sequencing on an NGS device (e.g. Illumina or Ion device). Only a single sequencing library needs to be constructed for 100’s to 1000’s of samples. Amplifications require a small amount of genomic DNA (or cDNA) – usually 40 to 80ng total for gDNA and as low as 4ng cDNA for human samples. Amplicon targets can be anywhere in the nuclear, mitochondrial or chloroplast genome.
Compared to indirect (or restriction-site mediated) methods for screening polymorphism or gene expression (e.g. qPCR, time-of-flight, size-based, GBS, RAD), the targeted-sequence-based approach is truly incredible. And, it’s much less expensive. For many of our projects, the total cost per data point is between $0.01 and $0.03 (pennies).
Current projects include large and small mammals (e.g. human, mouse), plants (e.g. taro, grass), plant diseases (many), and insects (e.g. thrips, army worm and midge).
MonsterPlex works well for targeted-RNAseq applications (gene profiling) from archived FFPE and fresh tissues. The dynamic range is almost unlimited – it’s up to you to choose how wide you want your window of analysis.
Our most recent success was screening mice for CRISPR/Cas9 induced INDELs and it worked great for deletions at or near the tag site that were between 1 and 50bp in length.