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7 years ago Alex Snyder says Affy can handle 1 ng of RNA! Connected me with Aaron Llanso.
The Clariom D Array is what we’ve run with Alex. The array generates a hypothesis-free, high resolution profile (nearly 7M probes) of all known transcript isoforms, both coding and non-coding: >540,000 transcripts covered in total. There are 10-15 probes across each exon, as well as exon-exon junction probes enabling deep alternative-splicing analysis. We can work with inputs down to 100pg of total RNA.
Once we get a quote together, I’ll initiate a new project with our service lab. They send you barcoded plates and protocols to send us the RNA. Once we receive it, we’ll do initial QC and share this along with our interpretation for final approval to move forward. From there, it’s typically ~3-4 weeks to get your data back. We can schedule our local field application scientist to do a first-pass at data analysis with you, and come in and help the lab learn how to use the software.
Clariom D projects typically run in $600/sample ballpark at CRO/core facilities, but we’re helping defray this by sharing labor costs for proof of principal immuno-oncology projects in our service lab.
There’s a few advantages to Clariom over RNAseq at 100M reads, and it really comes down to the level of analysis you’re after:
- Smaller input requirement, and able to handle lower quality input (FFPE, etc) – helping save banked clinical samples
- Clariom D has been shown to be roughly equivalent to >300M reads, generating higher resolution data and uncovering alternative splicing and lncRNA biology
- A hybridization approach, rather than a read-sampling sequencing technique (at this depth), provides better sensitivity for detection of rare variants, and small (often immunologically relevant) changes between rare populations within a sample.
If you’re primarily interested in gene-level expression, we have a lower cost Clariom S array, which has fewer probes per exon and no exon-exon junction probes. This would be more equivalent to the 100M read sequencing approach, although it’s not yet available through our service lab. We do have core facilities and service groups that can run these samples for you - I can get pricing if you like.
I want to make sure we’re comparing apples to apples as best we can between the two approaches – you mentioned being able to do 100M RNAseq reads for roughly the same price as the Clariom D assay. Is this for paired-end sequencing?
We typically see a 100M paired end gene-level RNAseq project in the $1000/sample ballpark, whereas 30-40M reads would be more around $300. The Clariom S array is roughly equivalent to 100M paired end reads and therefore is substantially lower cost for the same resolution data (100M paired ends) in our experience. However, if this is not paired end sequencing, you’d be getting much higher quality gene-level data in the 50-100M read paired end range by using Clariom S. The SEQ-QC study recommends this range of paired end sequencing depth for good gene level data, and even higher (~90M) from the experiments testing the MAQC study’s titrated sample set.
If the subset of genes you are looking at is highly expressed, then read depth may not be as much a concern, though we see that labs are identifying potentially biologically relevant changes in lowly expressed genes and rare isoforms between immunologic cell lines, which is a primary reason we’ve recommended the Clariom D array for these types of studies. Clariom D is considered roughly equivalent to 300-700 million paired end reads (depending on replicates).
NGX Bio send me these names: