CONFIRM Sequence app fails to process phosphorothioate sequences - WKB305263

SYMPTOMS

• CONFIRM Sequence fails to process data when a phosphorothioate-linked oligonucleotide sequence is used in an analysis
• The same data can be processed if you use a phosphodiester-linked oligonucleotide sequence

ENVIRONMENT

• waters_connect 3.6.0
• waters_connect 3.7.0
• CONFIRM Sequence 1.4.0

CAUSE

An incompatibility between Confirm Sequence 1.4.0 and waters_connect base kits 3.6.0 and 3.7.0

The phosphorothioate monomer IDs contain an asterisk (*). The versions of platform services used in waters_connect 3.6.0 and 3.7.0 do not accept the presence of an asterisk in the monomer ID field of Confirm Sequence, so processing fails.

FIX or WORKAROUND

Perform an in-place upgrade to waters_connect 4.0.0.

NOTE : Because the issue arises from functionality in the base kit, the same version of Confirm Sequence that fails to process phosphorothioate sequences when installed with waters_connect 3.7.0 will successfully process phosphorothioate sequence when installed with waters_connect 4.0.0.

ADDITIONAL INFORMATION

The issue affects only the listed version of waters_connect base kit. It did not occur in Waters_connect 3.2.0, and it was fixed in waters_connect 4.0.0.

It is also possible to work around the issue in the affected version by manually creating an alternative set of phosphorothioate monomers.

1. Open the Synthetic Library app.
2. Open the Monomers library.
3. For each phosphorothioate monomer (that is, those with * in the ID field):
   1. Clone the monomer.
   2. Edit the ID field to contain only alphanumeric characters. For example: For deoxyadenosine thiophosphate, change the ID from "dA*" to "dAs".
   3. Save the cloned, edited monomer.
4. Open the oligonucleotide Sequence Library.
5. Edit each sequence containing phosphorothioate monomers to replace those containing asterisks with those created at step 3.
6. Open the mRNA Library.
7. Edit each sequence containing phosphorothioate monomers to replace those containing asterisks with those created at step 3.

If a customer uses the workaround and then upgrades to waters_connect 4.0.0, they can continue to use the alternative phosphorothioate monomers they created or go back to using the default phosphorothioate monomers installed with Confirm Sequence 1.4.0.

The issue in waters_connect 3.6.0 and 3.7.0  was logged as CRI-8171.