GPL-861 Plate map changes to support consolidated plates from Hamilton CP [Heron]

[rl15]

User story GPL-861 | As LIMS team we need to refine the plate map standard to support a change directed by consolidating plates and new robotics

Who are the primary contacts for this story Sonia G (PAM) Cristina A (PAM) Alan K (PAM)

Acceptance criteria To be considered successful the solution must allow:

• [x] New gene RNaseP & IEC for 'CHn-Target' (n in 1..4)
• [x] Parse Empty in addition to no value for 'Root Sample ID'; do not log, ignore any other row data
• [x] Parse Unknown for CT values (same as empty cell)
• [x] Parse consolidated plate map files with file name format described in additional context
• [ ] Lighthouse plate map standard document is updated to reflect changes
• [ ] change required in lighthouse service for sentinel process - if the lab ids are different for a plate it will fail
• [x] Ignore PickResult column and not log the error

Additional context

Lighthouse	Surveillance Barcodes Format	Surveillance Barcodes Example	Eagle Barcode Format	Eagle Barcode Example
Milton Keynes	XXXNNNNNN	RNA123456	XXXNNNNNN	EGL123456
Alderley Park	XX-XXX-NNNNNNNN	AP-rna-12345678	XXXNNNNNN	APE123456
Glasgow	XXXNNNNNNX	GLA123456R	XXXNNNNNN	EGG123456 GLS123456
Cambridge	NNNNNNNNN	123456789	XXXNNNNNN	EGC123456 CBE123456
Randox	XXX-AA-NNNNNNNN	RDX-J1-123456	XXXNNNNNN	RXE123456

• X: Letter Character (Upper or Lower case)
• A: Alphanumeric Character (Upper or Lower case)
• N: Number

NB Current state play: If the coordinate is put in a separate column rather than concatenated to the plate id, the row will fail.

Dan L Wrote (26 February 2021 12:03)

Thanks for confirming point 1,

and example file received on 26th Feb has well position e.g.: AP-rna-00195161_A01

Uncertainty

• From feedback on the 11th February from Dan J L (Deloitte) have remaining uncertainty to clarify.

• Result ‘Limit of detection’ may change.

• It would be extremely helpful if the Sanger can let me know the characters allowed for the filename – like A-Z, a-z, 0-9, and the special characters allowed, it would give us some flexibility while still able to support Sanger requirements.

  Assume we would need list of special characters to add this to regex.

• There is the as yet untested idea that special characters would be handled well by the SFTP sever itself.

[rl15]

Alan K wrote (Tuesday, 16 February 2021 at 12:15) This will be required once LHs shift to cp on site. Timeline for this is unknown but could be within the month

Q> Can we assume all the LH labs wil use the new file naming convention? - PSG

A. All LHs using Hamiltons will use this format (AP/MK/GLS) but hope that Randox and CAM will also align.

[rl15]

Alan K wrote(Thursday, 18 February 2021 at 10:18)

Q> Do you want us to prioritise this change?

Go-live looks like late next week at earliest. Is that a feasible timeline for you and the team? Understand things are manic currently so let me know.

Q> I assume all the LH labs will use the new file naming convention?

As I said before all LHs using Hamiltons will use this format (AP/MK/GLS). No current direction from Deloitte for other labs but will see if Randox and CAM will also align.

[rl15]

Alan K wrote (Friday, 19 February 2021 at 14:23)

One potential result of the testing (in simulation) is changing the naming convention of the output plates. I originally proposed the <purpose><barcodeID>.csv schema so LHLs can easily identify where to send each plate map. Yesterday we find out it may interfere with Hamilton’s logic to avoid accidental double picking into the same plate, so we may simplify the plate map filename to <barcodeID>.csv only and save different files into different sub-folders. Hence, would be great if Sanger can make the change to accommodate <barcodeID>.csvformat in future as well.

[rl15]

Dan L (Deloitte) wrote (26 February 2021 12:03)

Please find attached two example output files from AP (we used mock input plate maps for the testing that’s why lab IDs are GLS and CB). The filename is in line with general AP RNA plates – note this is only for general surveillance plates. For priority plates, per discussed on the earlier call, CB will print barcodes starting with EAP prefix and send to AP.

20210226_example_plate_maps.zip

Rich L: Observed when looking at the contents of the file:

• value of IEC in CH2_target (Current set is ORF1ab, N gene, S gene, MS2, E-Gene)
• Pick result column (which we will ignore)

[pjvv]

@rl15, Is the new gene ICE or IEC?

[pjvv]

@rl15

Parse “Unknown” for CT values (Same as empty cell)

Is that for all CT columns? Target, Result and Cq? Or just one of them?

[andrewsparkes]

@rl15 Is the PickResult column required for consolidated files? Should it be stored in MongoDB and MLWH? I suspect it indicates whether the cherrypick happened, to transfer the sample to the consolidated plate (Hamilton robots have liquid sensing). If so it should be used in the positive filtering rules (no point us trying to sequence something that wasn't transferred into the plate). Also what are the allowed values, we currently see 'Success' and 'Insufficient volume' in the example files.

[neilsycamore]

@rl15 Alan K via RT 713867 added 2 more Eagle prefix

Lab | Prefix AP | APE Randox | RXE

[pjvv]

From: Alan K Sent: 02 March 2021 14:04 To: Rich Livett Subject: RE: AP cherry picking pre go-live alignment [EXT]

Thanks Rich Corrections below:

Purpose is now no longer being used as a prefix so plate barcode will be the file name. Any accepted plate barcodes will need to be accepted as file name standards. Suggest start with Eagle varieties (XXXnnnnnn) and AP (for example AP-rna-00223715)

Lab	Prefix
CB	CBE
GLA	GLS
MK	EMK
AP	APE
Randox	RXE

[pjvv]

From: Alan K Date: Wednesday, 3 March 2021 at 11:59 To: Richard Livett Subject: RE: AP cherry picking pre go-live alignment [EXT]

Further update:

Randox now using plate barcode as file name as of 03/03.

Eg. RDX-J2-020035

[pjvv]

@rl15

1. I can't see an example of RNaseP, where is that coming from?

Dan L (Deloitte) wrote (Friday, 12 February 2021 at 19:07)

A quick summary on the agreements and actions:

Dan to ask Hamilton to add RNA ID column with _ format Sanger will accept individual plate maps Alan to check the filename restrictions on plate maps and feedback by Monday noon Sanger to remove validation on lab ID digits (if there is one) Sanger to expand CH-1 Target, CH-2 Target, CH-3 Target, CH-4 Target accepted vocabulary to accept at least RNaseP Dan to inform Sanger on future NPEx data changes (e.g. agreed term for PLOD) Sonia to share proposed Sanger requirements beyond data with Dan ASAP for validation

2. Should we track that we have parsed an Eagle plate somehow?

No. Discussed yesterday and PAM can am Eagle plate from the LH sample table bu prefix. Want to keep this light touch rather than add another col to the LH_sample table to start with. Identifying Eagle samples needs to come from entity external to Sanger.

[pjvv]

From: Alan K Date: Wednesday, 10 March 2021 at 10:36

Lighthouse	Surveillance Barcodes Format	Surveillance Barcodes Example	Eagle Barcode Format	Eagle Barcode Example
Milton Keynes	XXXNNNNNN	RNA123456	XXXNNNNNN	EGL123456
Alderley Park	XX-XXX-NNNNNNNN	AP-rna-12345678	XXXNNNNNN	APE123456
Glasgow	XXXNNNNNNXXXX-AA-NNNNNNNN	GLA123456R??	XXXNNNNNN	EGG123456 GLS123456
Cambridge	NNNNNNNNN	123456789	XXXNNNNNN	EGC123456 CBE123456
Randox	XXX-AA-NNNNNNNN	RDX-J1-123456	XXXNNNNNN	RXE123456

X= Letter Character (Upper or Lower case) A = Alphanumeric Character (Upper or Lower case) N = Number

[pjvv]

From: Alan K Date: Mon, 15 Mar 2021 12:45:17

Lighthouse	Surveillance Barcodes Format	Surveillance Barcodes Example	Eagle Barcode Format	Eagle Barcode Example
Milton Keynes	XXXNNNNNN	RNA123456	XXXNNNNNN	EGL123456
Alderley Park	XX-XXX-NNNNNNNN	AP-rna-12345678	XXXNNNNNN	APE123456
Glasgow	XXXNNNNNNX	GLA123456R	XXXNNNNNN	EGG123456 GLS123456
Cambridge	NNNNNNNNN	123456789	XXXNNNNNN	EGC123456 CBE123456
Randox	XXX-AA-NNNNNNNN	RDX-J1-123456	XXXNNNNNN	RXE123456