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HD-SSO technology for High-Res DNA typing
Posted: 18 August 2009 01:30 PM   [ Ignore ]  
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Hello~
Our lab has adopted the One Lambda HD-SSO system as the first step to reporting high-resolution DNA typing.  We are pleased with the results so far, but we are still gathering more information about the strengths, limits, range, and sensitivity of this system.  When we find a resulting allele pair that does not resolve to a single Common and Well-Documented allele or allele group, we use the O.L. allele-specific MicroSSP kits. In our hands so far, ~60% of all patient samples require secondary SSP tests to resolve one or more loci; average is 1.1 SSP tests/patient - very manageable so far.  While we’ve been having some PCR drama lately getting perfect results (due to DNA conc., well failures, dehydrated wells? etc.), we’re working through these and discussing options with the manufacturer.
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I’m wondering how many other labs are in our same situation. Would anyone would like to communicate and share notes/experiences using the HD-SSO and allele-specific SSP reagents for HR typing??
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Specifically, we’ve detected several allele pairs that just can’t be resolved to single CWD alleles using these reagents, and therefore must be sent out for SBT. It would be great to know about other situations like this, ones that we just haven’t run across yet.  We’d be happy to share more about our findings.
I’d appreciate replies to the forum or via personal email.
Thanks!
Carley Shaut

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Posted: 24 August 2009 05:14 PM   [ Ignore ]   [ # 1 ]  
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Here’s an example of an allele pair that we are not able to resolving using the available HD-SSO and allele-specific SSP trays (B*40 and B*44), and therefore will be sent for sequencing:
B*40DZFM(4001g) B*4402/4409/4441.  Unfortunately, the B*4441 overlaps by one bead with a B*40 allele, so this allele comes up as one possibility. This is the second time we’ve encountered this allele pair ambiguity.

Any suggestions or ways around this?

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