Thermo Scientific Appliedbiosystems SeqStudio Flex Series Manuale utente

For Research Use Only. Not for use in diagnostic procedures.

SeqStudio™Flex Series Genetic Analyzer with

Instrument Software v1.0

USER GUIDE

Catalog Numbers A50369

Publication Number 100104689

Revision A

Life Technologies Holdings Pte Ltd | Block 33 | Marsiling Industrial Estate Road 3 | #07-06, Singapore 739256

For descriptions of symbols on product labels or product documents, go to thermoﬁsher.com/symbols-deﬁnition.

The information in this guide is subject to change without notice.

DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC INC. AND/OR ITS AFFILIATE(S) WILL NOT BE

LIABLE FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR

ARISING FROM THIS DOCUMENT, INCLUDING YOUR USE OF IT.

Revision history: Pub. No. 100104689

Revision Date Description

A 26 January 2022 New document for SeqStudio™Flex Series Genetic Analyzer with

Instrument Software v1.0.

Important Licensing Information: These products may be covered by one or more Limited Use Label Licenses. By use of these

products, you accept the terms and conditions of all applicable Limited Use Label Licenses.

NOTICE TO PURCHASER: DISCLAIMER OF LICENSE: Purchase of this software product alone does not imply any license under any

process, instrument or other apparatus, system, composition, reagent or kit rights under patent claims owned or otherwise controlled by

Thermo Fisher Scientiﬁc, either expressly, or by estoppel.

TRADEMARKS: All trademarks are the property of Thermo Fisher Scientiﬁc and its subsidiaries unless otherwise speciﬁed.

Contents

■CHAPTER 1 Product information ................................................ 16

Product description ............................................................ 16

Precautions for use ........................................................ 17

Instrument components .................................................... 18

Instrument interior components ............................................. 21

Power and communication connections ...................................... 22

Theory of operation ............................................................ 23

Preparing samples ......................................................... 23

Preparing the instrument .................................................... 23

During a run ............................................................... 24

Results ................................................................... 24

Materials for routine operation ................................................... 24

Instrument consumables handling, usage limits, and expiration ...................... 25

Conﬁguring the instrument to prevent the use of consumables beyond

expiration and usage limits ................................................ 25

Important notice regarding use of consumables that exceed supported limits ..... 25

Buer storage, usage, and limits ............................................. 26

Polymer storage, usage, and limits ........................................... 26

Conditioning reagent storage, usage, and limits ............................... 27

Capillary array storage and usage ........................................... 27

Hi‑Di™Formamide storage and usage ........................................ 28

About the SeqStudio™Flex Series Instrument Software v1.0 ......................... 28

Proﬁle and sign in options .................................................. 29

Parts of the software ....................................................... 35

Companion software ....................................................... 49

Secondary analysis software ................................................ 50

Network connection options ..................................................... 51

Network and password security requirements ..................................... 52

Network conﬁguration and security .......................................... 52

Password security ......................................................... 52

SeqStudio™Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide 3

■CHAPTER 2 Get started .......................................................... 53

Proﬁle and sign in options ....................................................... 55

Create a local proﬁle (one time only) .......................................... 55

Switch user or sign out .................................................... 59

Workﬂow: Create a plate, start and monitor a run, then view results .................. 62

Prepare the instrument .......................................................... 64

Review upcoming maintenance .............................................. 64

Check consumables status ................................................ 66

Check instrument status ................................................... 67

Preheat the instrument oven and the detection cell ............................. 68

Check for leaks and spills ................................................... 68

Check buer ﬁll levels ...................................................... 70

Replenish consumables .................................................... 71

Ensure proper installation of CBC septa ...................................... 71

Control the LED light, speaker volume, and screen brightness ................... 72

■CHAPTER 3 Prepare the samples ................................................ 73

Sample preparation guidelines ................................................... 73

Plate and strip-tube layout ...................................................... 75

Prepare and assemble sample plates ............................................. 76

Prepare sample plates ...................................................... 76

Prepare the plate assembly ................................................. 77

■CHAPTER 4 Create a plate ﬁle on the instrument ............................. 83

Create, copy, or import a plate ﬁle ............................................... 83

Options for creating plate ﬁles ............................................... 83

Create a plate ﬁle .......................................................... 84

Copy a plate ﬁle ........................................................... 85

Import a plate ﬁle .......................................................... 86

Enter plate properties ........................................................... 88

Enter injection properties ........................................................ 89

Specify replicate injections ...................................................... 92

Enter sample names, sample types, and custom ﬁelds .............................. 93

Contents

4SeqStudio™Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide

■CHAPTER 5 Create a plate ﬁle in the Plate Manager software ................ 95

Options for creating plate ﬁles in the Plate Manager software ....................... 95

Get started with the Plate Manager software (desktop) ............................. 96

About the SeqStudio™Plate Manager 2.0 software (desktop) .................... 96

Access the Plate Manager software (desktop) ................................. 99

Parts of the Plate Manager software (desktop) home screen ................... 101

Connect the Plate Manager software (desktop) to an instrument ............... 103

Get started with the Plate Manager software (cloud) ............................... 105

About the SeqStudio™Plate Manager 2.0 Software (Thermo Fisher™Connect) ... 105

Access the Plate Manager software (cloud) .................................. 111

Parts of Plate Manager software (cloud) home screen ......................... 112

Connect Plate Manager software (cloud) to an instrument .................... 114

Set up a plate ﬁle ............................................................. 115

Create or open a plate ﬁle (PSM ﬁle) ........................................ 115

Enter plate properties ..................................................... 116

Enter sample and injection information ...................................... 116

Save a plate ﬁle .......................................................... 119

Keyboard shortcuts and examples .............................................. 121

Set up cloud analysis in the Plate Manager software (cloud) ....................... 124

Print the plate layout .......................................................... 125

Send a plate ﬁle to the Inbox on the instrument ................................... 126

Additional functions in the Plate Manager software ................................ 127

Load or download an example plate ﬁle ..................................... 127

Specify replicate injections (Add run module function) ........................ 128

Use the list view in the Plate tab ............................................ 128

Deﬁne custom ﬁelds ...................................................... 129

Save a plate ﬁle in CSV format ............................................. 129

Export or download a plate ﬁle in PSM format ................................ 129

Manage the software ...................................................... 131

■CHAPTER 6 Start and monitor a run .......................................... 136

Load and unload a plate ....................................................... 136

Load a plate into the instrument ............................................ 136

Unload a plate from the instrument ......................................... 139

Link a plate ﬁle and start a run .................................................. 140

Unlink a plate ﬁle ............................................................. 144

Processes that the instrument performs during a run .............................. 144

Pre-run check messages and plate alerts during a run ............................. 146

Pre-run checks when a plate run starts or a re-injection or a cancelled

injection is added to the Run queue ....................................... 146

Pre-run checks before each injection or when a paused run is resumed ......... 146

Contents

SeqStudio™Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide 5

Run plates with the automated barcode workﬂow ................................. 147

Create the plate ﬁles before the barcoded plates are loaded into the drawer ..... 147

Pre-run checks and plate alerts in an automated barcode run .................. 149

View alert and notiﬁcation details ............................................... 149

Auto-spectral calibration during an injection ...................................... 150

Auto-spectral calibration overview .......................................... 150

Auto-spectral calibration requirements ...................................... 151

Auto-spectral calibration results ............................................ 152

View real-time results in the home screen ........................................ 153

Pause the instrument in the home screen ........................................ 157

Use the Run queue to monitor a run on the instrument ............................ 160

Parts of the Run Queue screen ............................................. 160

View real-time results in the Run Queue screen .............................. 162

Change the injection list order .............................................. 163

Cancel or add injections or specify re-injections in the Run Queue screen ....... 165

Pause the instrument in the Run Queue screen ............................... 166

■CHAPTER 7 View results on the instrument ................................... 169

Options for viewing results on the instrument ..................................... 169

View results for a completed run (Run history).................................... 170

Export results from the instrument—Results and data ﬁles, logs, and reports ......... 171

Sample QC and quality alerts .................................................. 172

Use the electropherogram screen ............................................... 173

Sequence analysis results ...................................................... 175

Parts of the sequencing electropherogram screen ............................ 175

Sequencing results and well details ......................................... 176

Understanding Quality Values (QVs) ......................................... 178

Fragment analysis results ...................................................... 179

Parts of the fragment analysis electropherogram screen ....................... 179

Fragment analysis results and well details ................................... 180

■CHAPTER 8 Use the Remote Monitoring software to monitor runs,

view results, and use cloud analysis ........................................... 182

Monitor a run from the Remote Monitoring software ............................... 182

Open the Remote Monitoring software from the Plate Manager software (cloud) . 182

Open the Remote Monitoring software from the InstrumentConnect software .... 183

Parts of the Remote Monitoring software home screen ........................ 184

Plate ﬁle requirements for viewing analyzed and cloud results .................. 187

View instrument notiﬁcations in your Thermo Fisher™Connect account .......... 188

Set up email notiﬁcations from the instrument ................................ 189

View real-time results in the Remote Monitoring software ...................... 190

Sequencing results ....................................................... 192

Fragment analysis results .................................................. 192

Contents

6SeqStudio™Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide

Cancel injections or specify re-injections in the Remote Monitoring software .... 192

Pause the instrument from the Remote Monitoring screen, resume from the

instrument home screen ................................................. 193

Monitor a run from a mobile device .............................................. 193

Monitor a run from a mobile device ......................................... 195

View results in the Remote Monitoring software ................................... 198

View results for a completed run in the Remote Monitoring software (Run

History tab) ............................................................ 198

Export a results report from the Remote Monitoring software ................... 201

Download results from the Remote Monitoring software ....................... 201

Viewing spectral calibration or install run results in the Remote

Monitoring software ..................................................... 202

Use cloud analysis in the Remote Monitoring software ............................. 202

Automated cloud analysis with secondary analysis software ................... 202

Workﬂow: cloud analysis .................................................. 203

Set up cloud analysis for a completed run in the Remote Monitoring software .... 205

Access cloud analysis results from the Remote Monitoring software ............ 207

■CHAPTER 9 Use the instrument with Thermo Fisher™Connect ............. 210

Overview of Thermo Fisher™Connect features .................................... 211

Administrator set up for Thermo Fisher™Connect ................................. 211

User set up for Thermo Fisher™Connect ......................................... 212

Local proﬁle and cloud proﬁle: when to use, user name, and user initials ............. 213

(Recommended) Link directly to your Thermoﬁsher.com account ................... 217

Link a local proﬁle to your Thermoﬁsher.com account (one time) .................... 220

Re-link the instrument to your cloud proﬁle ....................................... 223

Disconnect the instrument from your cloud proﬁle ................................. 224

Change your cloud proﬁle PIN ................................................. 225

Set up email notiﬁcations from the instrument .................................... 226

Tasks for the cloud administrator of an instrument ................................ 228

Enable or disable Thermo Fisher™Connect access on the instrument

(administrator only) ..................................................... 228

Thermo Fisher™Connect cloud administrator functions ........................ 229

Manage the users and administrators of your instrument ...................... 229

Change the instrument name in the InstrumentConnect software (cloud

administrator only) ...................................................... 230

For more information on using Thermo Fisher™Connect ........................... 231

Use voice commands ......................................................... 231

Enable (register) the voice command function ................................ 231

Disable the voice command function ........................................ 232

Use voice commands ..................................................... 232

Contents

SeqStudio™Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide 7

Basic voice commands .................................................... 234

Interactive voice command—start run ....................................... 234

Microphone icon indicators for voice commands .......................... 235

■CHAPTER 10 Use the instrument with the Security, Auditing, and

E‑signature (SAE) v2.1 module ................................................. 237

Overview of the Security, Auditing, and E‑signature (SAE) v2.1 module components ... 238

Conﬁguring the SAE module and setting permissions .............................. 239

Functions that are not available when the SAE module is enabled ................... 240

Enable SAE mode on the instrument and specify the SAE server (administrator only) .. 240

Disable SAE mode on the instrument (administrator only) .......................... 243

Audit reason requirements ..................................................... 245

E-signature requirements for starting a spectral, install, or regular run ............... 245

Signing an object before a regular run is started .................................. 246

Signing an object when a regular run is started ................................... 247

Signing during an automated barcode run ........................................ 249

Displaying signatures .......................................................... 249

Use the instrument when the SAE server is oine ................................. 250

SAE error messages and actions ................................................ 251

■CHAPTER 11 Manage library resources on the instrument ................. 252

Overview of libraries ........................................................... 253

General library procedures ..................................................... 255

Create a new entry from a factory-provided or locked entry .................... 255

Lock or unlock a library entry ............................................... 255

Copy a library entry ....................................................... 255

Edit a library entry ........................................................ 256

Import a library entry ...................................................... 256

Export a library entry ...................................................... 256

Filter library lists .......................................................... 257

Delete a library entry ...................................................... 258

Plate ﬁles library ............................................................. 258

Plate ﬁle deﬁnition ........................................................ 258

Create a plate ﬁle ......................................................... 259

Deﬁne custom ﬁelds ...................................................... 262

Export or delete a plate ﬁle ................................................ 264

Import a plate setup from a CSV or PSM ﬁle ................................. 264

Plate ﬁle Properties tab ................................................... 265

Plate ﬁle Plate tab ........................................................ 267

Plate ﬁle Edit Injection Properties screen .................................... 268

Plate ﬁle Edit Well Properties screen (sample name entry) ..................... 271

Contents

8SeqStudio™Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide

Run modules library ........................................................... 272

Run module overview ..................................................... 272

Run module provided ..................................................... 272

Create a new run module ................................................. 272

Run module settings ...................................................... 273

Size standards library ......................................................... 275

Size standard overview .................................................... 275

Size standard deﬁnition ﬁles provided ....................................... 275

Create a new size standard ................................................ 276

Modify a factory-provided normalization size standard ........................ 277

Size standard normalization feature ......................................... 278

File Name Conventions library ................................................. 278

File name convention overview ............................................. 278

Create a new ﬁle name convention .......................................... 279

File name convention settings .............................................. 282

Injection protocols library ...................................................... 283

Injection protocol overview ................................................ 283

Create a new injection protocol ............................................ 283

Injection protocol settings ................................................. 284

Dye sets library .............................................................. 285

Dye set overview ......................................................... 285

Create a new dye set ...................................................... 285

Create a custom dye set ................................................... 286

Dye set settings .......................................................... 286

Analysis settings library ....................................................... 288

Analysis settings overview ................................................. 288

Create a new analysis settings ............................................ 289

Analysis settings—Sequencing ............................................. 291

Analysis settings—Fragment analysis ....................................... 295

Results Groups library ........................................................ 301

Results group overview .................................................... 301

Create a new results group ................................................ 302

■CHAPTER 12 Run calibrations and install checks ............................ 304

Run a spatial calibration ....................................................... 304

Spatial calibration overview ................................................ 304

When to perform a spatial calibration ........................................ 304

Perform a spatial calibration ............................................... 305

Evaluate the spatial calibration results ....................................... 306

Contents

SeqStudio™Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide 9

Example spatial proﬁles ................................................... 308

Export spatial calibration results or report .................................... 309

Run a spectral calibration ...................................................... 310

Overview of spectral calibration ............................................ 310

When to perform a spectral calibration ...................................... 311

System dye sets versus custom dye sets .................................... 312

Using BigDye™Direct Cycle Sequencing Kit chemistry ........................ 312

Estimated spectral calibration run times ..................................... 313

Prepare for custom dye set spectral calibration .............................. 314

Prepare for spectral calibration ............................................. 314

Perform a spectral calibration .............................................. 316

View spectral calibration results ............................................ 317

Example spectral calibration data ........................................... 324

Export spectral calibration logs or report .................................... 325

View and export the spectral calibration history .............................. 326

Perform an install run .......................................................... 328

Overview of install run ..................................................... 329

When to perform an install run ............................................. 329

Estimated install run times ................................................. 330

Prepare for the install run .................................................. 330

Perform an install run ..................................................... 333

View sequencing install run results .......................................... 334

View fragment analysis install run results .................................... 347

View, export, or delete an install run history ................................. 352

■CHAPTER 13 Maintain the Instrument ......................................... 354

Maintenance schedule ......................................................... 354

Review upcoming maintenance ............................................ 355

Daily instrument maintenance tasks ......................................... 356

Monthly instrument maintenance tasks ...................................... 357

Annual planned maintenance tasks ......................................... 358

As-needed instrument maintenance tasks ................................... 358

Maintenance wizard overview .................................................. 359

Clean the instrument .......................................................... 361

Export consumables log ﬁles ................................................... 363

Install buers (wizard) ......................................................... 363

Install the anode buer container (ABC) ..................................... 364

Install the cathode buer container (CBC) ................................... 367

Replenish, change, ﬂush, and store polymer (wizards) ............................. 370

Precautions for use ....................................................... 370

Replenish polymer or change polymer type (wizard) ........................... 370

Store partially used polymer ............................................... 371

Contents

10 SeqStudio™Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide

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