Thermo Fisher Scientific CytoScan HT-CMA Assay 96-Array Format Automated Workflow User guide

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

CytoScan™ HT-CMA Assay 96-Array Format

Automated Workﬂow

USER GUIDE

for use with:

CytoScan™ HT-CMA 96-Array Plate

Applied Biosystems™ HT Target Prep Reagent Kit 96F

Applied Biosystems™ NIMBUS™ Target Preparation Instrument

Catalog Numbers 906019 and 906024

Publication Number MAN0018211

Revision D.0

Manufacturer:

Thermo Fisher Scientiﬁc Baltics UAB |

V.A. Graiciuno 8, LT-02241 |

Vilnius, Lithuania

Products:

Applied Biosystems™ HT Target Prep Reagent Kit 96F

Manufacturer:

Aymetrix Pte Ltd |

7 Gul Circle #2M-01 |

Keppel Logistics Building |

Singapore 629563

Products:

CytoScan™ HT-CMA 96-Array Plate

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. MAN0018211

Revision Date Description

D.0 29 April 2021 •Added options for using alternative 96-well round deepwell plates and 96-well PCR plates.

•Added requirements for HT Target Prep 96 Consumables Kit for Applied Biosystems™ NIMBUS™ 2.0, v2.

•Changed starter kit to HT Target Prep NIMBUS Starter Kit.

•Changed method name to Automated HT Target Preparation Solution.

C.0 13 October 2020 • Updated reagent kit name to Applied Biosystems™ HT Target Prep Reagent Kit 96F.

• Changed plate requirement from Eppendorf™ Deepwell Plate 96 to Axygen™ 96-well Round Deepwell

Plate.

• Added missing steps to Prepare the GeneTitan™ MC Instrument.

• Changed time to 50 minutes to bring plate to room temperature in Hyb-Wash.

• Standardized plate names throughout.

B.0 04 February 2020 Adding information for Windows™ 10 users.

A.0 13 November 2019 New document.

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.

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

trademark and brand of Alpaqua Engineering, LLC. Axygen is a registered trademark of Corning Incorporated. BINDER is a trademark

of BINDER GmbH. Bio-Rad, Microseal, DNA Engine Tetrad, and Hard-Shell are registered trademarks of Bio-Rad Laboratories, Inc.

Boekel and Jitterbug are trademarks of Boekel Scientiﬁc. Cermax is trademark of Excelitas Technologies. Eppendorf and Mastercycler

are registered trademarks of Eppendorf AG. Hamilton, CO-RE, Microlab, NIMBUS, and Hamilton are owned and/or registered by

Hamilton Company in the U.S. and/or other countries. Microsoft, and Excel are either registered trademarks or trademarks of Microsoft

Corporation in the United States and/or other countries. PerkinElmer is a registered trademark of PerkinElmer, Inc. SpectraMax is a

registered trademark of Molecular Devices Corporation.

Contents

■CHAPTER 1 Overview ............................................................. 10

Introduction ................................................................... 10

About the CytoScan™ HT-CMA Assay 96-Array Format Automated Workﬂow .......... 11

Assay highlights ........................................................... 11

Multiplate workﬂows ........................................................... 12

Overview of the CytoScan™ HT-CMA Assay 96-Array Format Automated

Workﬂow on the NIMBUS™ Instrument .......................................... 13

■CHAPTER 2 Genomic DNA preparation ......................................... 14

Sources of genomic DNA ....................................................... 14

General requirements ........................................................... 15

Special requirements ....................................................... 15

Evaluate the quality of genomic DNA with 1% agarose E‑Gel™.................. 16

Genomic DNA extraction and puriﬁcation methods ................................. 17

Genomic DNA cleanup ......................................................... 18

Genomic DNA preparation ...................................................... 18

Genomic DNA input requirements ........................................... 18

Time required ............................................................. 18

Equipment, consumables, and reagents required .............................. 19

Thaw samples and control .................................................. 20

Quantify and dilute test sample gDNA ........................................ 20

Aliquot diluted samples and the Genomic DNA Standard (Ref 103) control to

the deepwell plate ....................................................... 20

Freeze or proceed ......................................................... 21

GeneTitan™ Array Plate Registration ﬁle ........................................... 21

Create and save a GeneTitan™ Array Plate Registration ﬁle ...................... 21

■CHAPTER 3 Set up the Applied Biosystems™ NIMBUS™ Target

Preparation Instrument ............................................................ 23

Required materials ............................................................. 23

Plate centrifuge ............................................................ 23

Labware used on the deck .................................................. 24

HT Target Prep Reagent Kit 96F ............................................. 29

Consumables required for target preparation .................................. 30

CytoScan™ HT-CMA Assay 96-Array Format Automated Workﬂow User Guide—Applied Biosystems™ NIMBUS™ Instrument 3

Pipette tips ............................................................... 30

Axiom™ GeneTitan™ Consumables Kit ........................................ 31

Guidelines for use .............................................................. 34

Guidelines for handling plates and tubes ...................................... 34

Guidelines for a run on the NIMBUS™ Instrument .............................. 35

Thermal cycler recommendations and protocol ................................ 35

Deck setup for reagent tubes .................................................... 36

Cooling block template ..................................................... 36

Assemble the cooling block template with reagent tubes and tube collar .......... 36

■CHAPTER 4 Target preparation with the Applied Biosystems™

NIMBUS™ Target Preparation Instrument ....................................... 38

Stage 1: Amplify the genomic DNA ............................................... 39

Time required ............................................................. 39

Input required ............................................................. 39

Materials, labware, and reagents required ..................................... 39

Perform the prerun checklist ................................................ 40

Prepare for DNA ampliﬁcation ............................................... 42

Run the DNA ampliﬁcation step .............................................. 43

Workﬂow for Stage 1: DNA ampliﬁcation ...................................... 48

Stage 2: Fragment and precipitate the DNA ....................................... 51

Time required ............................................................. 51

Input required ............................................................. 51

Materials, labware, and reagents required ..................................... 51

Perform the prerun checklist ................................................ 53

Prepare for fragmentation ................................................... 54

Run the fragmentation step, then precipitate samples .......................... 55

Workﬂow for Stage 2: Fragment and precipitate the DNA ....................... 60

Stage 3: Centrifuge and dry pellets ............................................... 64

Time required ............................................................. 64

Input required ............................................................. 64

Equipment and consumables required ........................................ 64

Centrifuge and dry the pellets ............................................... 64

Stage 4A and 4B: Resuspension and hybridization preparation ...................... 66

Time required ............................................................. 66

Input required ............................................................. 66

Materials, labware, and reagents required ..................................... 66

Thaw reagents ............................................................ 68

Stage 4A: Prepare the resuspension buer ........................................ 69

Prepare pellets and Resuspension Buer ..................................... 69

Perform the prerun checklist ................................................ 69

Prepare resuspension reagents .............................................. 70

Run the resuspension step .................................................. 71

Contents

4CytoScan™ HT-CMA Assay 96-Array Format Automated Workﬂow User Guide—Applied Biosystems™ NIMBUS™ Instrument

Resuspend the samples by o-deck shaking .................................. 74

Workﬂow for Stage 4A: Resuspension ........................................ 75

Stage 4B: Prepare Hybridization Master Mix ....................................... 76

Perform the prerun checklist ................................................ 76

Prepare hybridization preparation reagents .................................... 77

Run the hybridization preparation step ....................................... 77

Workﬂow for Stage 4B: Prepare Hybridization Master Mix ....................... 81

Stage 4C: Perform sample QC ................................................... 83

Time required ............................................................. 83

Input required ............................................................. 83

Materials, labware, and reagents required ..................................... 83

Perform the prerun checklist ................................................ 84

Prepare the Hyb-Ready Plate ................................................ 85

Prepare gel diluent ......................................................... 86

Run the sample QC step .................................................... 86

Workﬂow for Stage 4C: Sample QC .......................................... 89

Stage 5: Prepare the hybridization tray ............................................ 91

About Stage 5: Prepare the hybridization tray ................................. 91

Time required ............................................................. 91

Input required ............................................................. 91

Materials, labware, and reagents required ..................................... 92

Perform the prerun checklist ................................................ 92

Sample plate and array plate preparation ..................................... 93

Prepare the GeneTitan™ MC Instrument ...................................... 94

Denature the hybridization-ready samples .................................... 95

Run the prepare hybridization tray step ....................................... 96

Load the hybridization tray and array plate into the GeneTitan™ MC Instrument .... 98

Workﬂow for Stage 5: Prepare the hybridization tray ............................ 98

Stage 6: Prepare GeneTitan™ reagent plates ....................................... 99

Time required ............................................................. 99

Materials, labware, and reagents required ..................................... 99

Guidelines for handling reagents with precipitates ............................ 102

Perform the prerun checklist ............................................... 103

Run the prepare GeneTitan™ reagent plates step ............................. 105

Stages 5 and 6 for a multiplate workﬂow .................................... 111

Workﬂow for Stage 6: Prepare GeneTitan™ reagent plates ..................... 113

■CHAPTER 5 Process array plates with the GeneTitan™ Multi-Channel

(MC) Instrument .................................................................. 120

Stage 1: Create and upload a GeneTitan™ Array Plate Registration ﬁle ............... 120

Stage 2: Hybridize plates in the GeneTitan™ MC Instrument ........................ 122

Materials, labware, and reagents required .................................... 122

Set up the instrument ..................................................... 123

Load an array plate and hybridization tray into the GeneTitan™ MC

Instrument (for Hyb-Wash-Scan or Hyb-Wash) ............................. 127

Contents

CytoScan™ HT-CMA Assay 96-Array Format Automated Workﬂow User Guide—Applied Biosystems™ NIMBUS™ Instrument 5

Load a second array plate and hybridization tray onto the GeneTitan™

MC Instrument ......................................................... 130

Queue a second plate for scanning ......................................... 132

Stage 3: Ligate, wash, stain, and scan ........................................... 134

The GeneTitan™ tray loading process ....................................... 134

Load trays in the GeneTitan™ Instrument .................................... 134

Continue the scan workﬂow .................................................... 139

Shut down the GeneTitan™ MC Instrument ....................................... 140

■CHAPTER 6 8-plate workﬂow for CytoScan™ HT-CMA Array Plates ........ 141

Overview of the 8-plate workﬂow ............................................... 142

Time required for assay steps .............................................. 144

Thaw the frozen plates of ampliﬁed DNA ..................................... 145

Thaw plates with frozen pellets ............................................. 146

Target preparation and array processing for the 8-plate workﬂow ................... 146

Day 1 activities ........................................................... 146

Day 2 activities ........................................................... 149

Day 3 activities ........................................................... 152

Day 4 activities ........................................................... 156

Day 5 activities ........................................................... 159

■CHAPTER 7 3-plate workﬂow for CytoScan™ HT-CMA Array Plates

with a 3-hour DNA precipitation step .......................................... 163

Overview of the 3-plate workﬂow with 3-hour precipitation ......................... 163

Time required for assay steps .............................................. 165

Thaw the frozen plate of ampliﬁed DNA ...................................... 167

Target preparation and array processing for the 3-plate workﬂow using a 3-hour

precipitation step ........................................................... 168

Day 1 activities ........................................................... 168

Day 2 activities ........................................................... 170

Day 3 activities ........................................................... 173

Day 4 activities ........................................................... 176

■CHAPTER 8 3-plate workﬂow for CytoScan™ HT-CMA Array Plates

with an overnight DNA precipitation step ...................................... 178

Overview of the 3-plate workﬂow with overnight precipitation ....................... 179

Time required for assay steps .............................................. 181

Thaw the frozen plate of ampliﬁed DNA ...................................... 183

Target preparation and array processing for the 3-plate workﬂow with an

overnight precipitation step .................................................. 184

Day 1 activities ........................................................... 184

Day 2 activities ........................................................... 186

Day 3 activities ........................................................... 188

Contents

6CytoScan™ HT-CMA Assay 96-Array Format Automated Workﬂow User Guide—Applied Biosystems™ NIMBUS™ Instrument

Day 4 activities ........................................................... 191

Day 5 activities ........................................................... 194

■APPENDIX A Recommended techniques for GeneTitan™ MC

Instrument operation ............................................................ 196

Array plate packaging ......................................................... 196

Proper tray alignment and placement ........................................... 197

Scan tray ................................................................ 199

Proper orientation of consumables .......................................... 200

Drawer tabs in the GeneTitan™ MC Instrument ............................... 201

Stain trays and covers ......................................................... 202

Label GeneTitan™ hybridization and reagent trays ................................. 202

Label the GeneTitan™ 96-layout hybridization tray ............................ 202

Label the GeneTitan™ reagent trays ......................................... 203

Deionization of GeneTitan™ trays and covers ..................................... 203

Deionize GeneTitan™ trays and covers ...................................... 205

Ion-indicator cap ......................................................... 206

Setup options for array plate processing ......................................... 206

Hyb-Wash-Scan .......................................................... 207

Hyb-Wash ............................................................... 207

Wash-Scan .............................................................. 208

Wash-Scan Resume ...................................................... 208

Scan .................................................................... 209

Unload Plates ............................................................ 209

Wash ................................................................... 209

When to abort a process ....................................................... 209

Abort a process .......................................................... 210

Email notiﬁcations from the GeneTitan™ MC Instrument ............................ 211

GeneTitan™ MC Instrument lamp ............................................... 212

■APPENDIX B Register samples in GeneChip™ Command Console™....... 213

GeneTitan™ Array Plate Registration ﬁle .......................................... 213

Create a GeneTitan™ Array Plate Registration ﬁle .................................. 213

■APPENDIX C Fragmentation quality control gel protocol .................... 216

Equipment required ........................................................... 216

E‑Gel™ and reagents required .................................................. 216

Consumables required ......................................................... 217

Prepare the gel diluent ......................................................... 217

Dilute the TrackIt™ Cyan/Orange Loading Buer .............................. 217

Dilute the 25 bp DNA ladder ............................................... 217

Run the fragmentation QC gel .................................................. 217

Contents

CytoScan™ HT-CMA Assay 96-Array Format Automated Workﬂow User Guide—Applied Biosystems™ NIMBUS™ Instrument 7

■APPENDIX D Sample quantiﬁcation after resuspension ..................... 219

Equipment required ........................................................... 219

Spectrophotometer ....................................................... 219

Quantify the diluted samples ................................................... 219

OD yield evaluation guidelines .................................................. 219

Plate reader guidelines for sample quantiﬁcation .................................. 220

■APPENDIX E Troubleshooting .................................................. 221

GeneTitan™ MC Instrument support ﬁles for troubleshooting ....................... 221

Log ﬁles ................................................................. 221

GeneChip™ Command Console™ log ﬁles .................................... 221

Other GeneChip™ Command Console™ ﬁles ................................. 221

GCC log ﬁles for GeneTitan™ MC Instrument systems ......................... 222

Troubleshooting the GeneTitan™ Multi-Channel Instrument ......................... 222

GeneTitan™ MC Instrument ﬂuidic diagnostic messages ........................... 225

■APPENDIX F GeneTitan™ Multi-Channel Instrument care .................... 228

Overview .................................................................... 228

Maintenance ................................................................. 228

Monthly ................................................................. 228

Every 6 months ........................................................... 229

Outer enclosure fan ﬁlters ...................................................... 229

Cleaning schedule ........................................................ 229

Clean the GeneTitan™ MC Instrument fan ﬁlter ............................... 229

Bottle ﬁlter replacement ....................................................... 230

Remove and inspect the reagent bottle ﬁlters ................................ 230

Replace ﬂuidics bottle ﬁlter ................................................ 231

Xenon lamp replacement in the GeneTitan™ MC Instrument ........................ 231

Lamp life/imaging device status notices ..................................... 231

Remove the xenon lamp ................................................... 233

Replace the xenon lamp ................................................... 234

Reset the lamp life counter ................................................ 235

Contents

8CytoScan™ HT-CMA Assay 96-Array Format Automated Workﬂow User Guide—Applied Biosystems™ NIMBUS™ Instrument

■APPENDIX G Routine care for the Applied Biosystems™ NIMBUS™

Target Preparation Instrument .................................................. 236

O-ring care ................................................................... 236

Tip isolator ................................................................... 237

Clean the tip isolator ...................................................... 238

Trash chute .................................................................. 239

Assemble the trash chute .................................................. 239

Trash chute cleaning ...................................................... 242

Thermoshake device maintenance .............................................. 243

■APPENDIX H Safety ............................................................. 244

Symbols on this instrument .................................................... 244

Standard safety symbols .................................................. 244

Location of safety labels ................................................... 246

Control and connection symbols ........................................... 247

Conformity symbols ...................................................... 248

Safety information for instruments not manufactured by Thermo Fisher Scientiﬁc ..... 249

Instrument safety ............................................................. 249

General ................................................................. 249

Physical injury ............................................................ 250

Electrical safety .......................................................... 251

Cleaning and decontamination ............................................. 252

Instrument component and accessory disposal .............................. 252

Safety and electromagnetic compatibility (EMC) standards ......................... 253

Safety standards ......................................................... 253

EMC standards ........................................................... 253

Environmental design standards ............................................ 254

Chemical safety .............................................................. 255

Biological hazard safety ....................................................... 256

■Documentation and support ...................................................... 257

Related documentation ........................................................ 257

Customer and technical support ................................................ 258

Limited product warranty ...................................................... 259

Contents

CytoScan™ HT-CMA Assay 96-Array Format Automated Workﬂow User Guide—Applied Biosystems™ NIMBUS™ Instrument 9

Overview

Cytogenetics studies are performed to identify structural changes in DNA, such as copy number

changes. Individuals typically have 2 copies of the genome in each of their cells: 1 inherited from

the mother, and 1 inherited from the father. Chromosomal abnormalities are common in several disease

states such as:

•Deletions—When 1 or both copies of a particular chromosome region are lost.

•Gains—When a chromosome or chromosomal region is duplicated or multiplied.

•Uniparental disomies (UPDs)—When 2 copies of a chromosome or chromosomal region are

present, but both have been inherited from a single parent.

The Applied Biosystems™ CytoScan™ HT-CMA Assay has been optimized for the detection of these

chromosomal abnormalities and does so in a high throughput format. The assay is used with genomic

DNA from blood or amniotic ﬂuid samples. The CytoScan™ HT-CMA Assay includes arrays and reagents

in either a 96- or 24‑sample format for use on the GeneTitan™ Multi-Channel Instrument. The high-

throughput nature of CytoScan™ HT‑CMA teamed with the intuitive Reproductive Health Research

Analysis Software (RHAS) enables you to perform high-resolution genome-wide copy number analysis

faster and easier than before. The combined high-resolution DNA copy number data and the ability to

screen a panel of single nucleotide variants (SNVs) on a single array makes the CytoScan™ HT-CMA

Assay the new standard for high throughput cytogenetics analysis.

Introduction

CytoScan™ HT-CMA Assay 96-Array Format Automated Workﬂow is available as a bundled kit that

includes the arrays, reagents, and consumables needed for processing one 96-array format plate. The

automated workﬂow that is described in this user guide uses the Automated HT Target Preparation

Solution method on the Applied Biosystems™ NIMBUS™ Target Preparation Instrument and for the

GeneTitan™ reagent preparation to process 96 samples at a time.

The CytoScan™ HT-CMA Assay interrogates biallelic and multiallelic SNPs, indels, and copy number

variation (CNV) in a single assay workﬂow. Starting with genomic DNA, the samples are processed by

performing an automated target preparation protocol followed by automated processing of the array

plates on the GeneTitan™ Multi-Channel (MC) Instrument.

•Target preparation uses methods including DNA ampliﬁcation, fragmentation, puriﬁcation, and

resuspension of the target in the hybridization cocktail.

•The hybridization-ready targets are then transferred to the GeneTitan™ MC Instrument for

automated, hands-free processing including hybridization, staining, washing, and imaging.

Array plates are processed on a GeneTitan™ MC Instrument controlled by Applied Biosystems™

GeneChip™ Command Console™ 4.3 or newer. The resulting CEL ﬁles are then analyzed by

Reproductive Health Research Analysis Software and Chromosome Analysis Suite.

1

10 CytoScan™ HT-CMA Assay 96-Array Format Automated Workﬂow User Guide—Applied Biosystems™ NIMBUS™ Instrument

About the CytoScan™ HT-CMA Assay 96-Array Format

Automated Workﬂow

The CytoScan™ HT-CMA Assay 96-Array Format Automated Workﬂow is a fully automated workﬂow for

high-throughput that requires the following sets of steps:

1. Genomic DNA preparation—Resulting in samples that meet requirements detailed in Chapter 2,

“Genomic DNA preparation”.

2. Automated target preparation of the samples (see Chapter 4, “Target preparation with the Applied

Biosystems™ NIMBUS™ Target Preparation Instrument”).

3. Array processing, done with:

•GeneTitan™ MC Instrument

•GeneTitan™ Instrument Control software

•Applied Biosystems™ GeneChip™ Command Console™ Portal software

See Chapter 5, “Process array plates with the GeneTitan™ Multi-Channel (MC) Instrument”.

A list of the required equipment and supplies for running the CytoScan™ HT-CMA Assay 96-Array

Format Automated Workﬂow on the Applied Biosystems™ NIMBUS™ can be found in the CytoScan™

HT-CMA Assay 96-Array Format Automated Workﬂow Site Preparation Guide—Applied Biosystems™

NIMBUS™ Instrument, Pub. No. MAN0018212.

Assay highlights

This user guide describes an option for a 3-hour DNA target precipitation step to enable a faster assay

turnaround time, going from sample to CEL ﬁle generation within 72 hours. The 3-hour precipitation

step shortens “Stage 2: Fragment and precipitate the DNA” on page 51 to enable the operator

to advance to “Stage 3: Centrifuge and dry pellets” on page 64, followed by “Stage 4A and

4B: Resuspension and hybridization preparation” on page 66, “Stage 4C: Perform sample QC” on

page 83, and the start of “Stage 5: Prepare the hybridization tray” on page 91 to start hybridization

on the GeneTitan™ MC Instrument on day 2 of the assay workﬂow. Note that this workﬂow option

requires approximately 9–10 hours to complete the combined day 2 activities (fragmentation to initiation

of hybridization on the GeneTitan™ MC Instrument).

In addition, a recommended workﬂow is presented to support the processing of 3 plates per week

using the shortened DNA precipitation step. This standard CytoScan™ HT-CMA Assay workﬂow,

in which the DNA is precipitated overnight, provides a convenient stopping point to support single-

operator assay execution of 1 plate within an 8-hour workday. See Chapter 7, “3-plate workﬂow for

CytoScan™ HT-CMA Array Plates with a 3-hour DNA precipitation step” for details regarding equipment

and operator assumptions to support this workﬂow.

Recommended workﬂows are presented to support the processing of 3 plates per week using 3-

hour DNA precipitation, and 8 plates per week using the standard overnight DNA precipitation. See

the appropriate chapter for details regarding equipment and operator assumptions to support these

workﬂows.

•Chapter 7, “3-plate workﬂow for CytoScan™ HT-CMA Array Plates with a 3-hour DNA precipitation

step”

•Chapter 6, “8-plate workﬂow for CytoScan™ HT-CMA Array Plates”

Chapter 1 Overview

About the CytoScan™ HT-CMA Assay 96-Array Format Automated Workﬂow 1

CytoScan™ HT-CMA Assay 96-Array Format Automated Workﬂow User Guide—Applied Biosystems™ NIMBUS™ Instrument 11

Multiplate workﬂows

Thermo Fisher Scientiﬁc supports high-throughput workﬂows that allow you to run a set of samples and

array plates through the protocol using a minimum number of personnel in a 40-hour week. The timing

of steps is critical because of the following limits:

•Incubation for DNA ampliﬁcation is 22–24 hours.

•Hybridization in the GeneTitan™ MC Instrument is 23.5–24 hours.

•Reagent trays for wash/stain/imaging must be prepared as hybridization ﬁnishes.

•Limits to when a second hybridization tray and array plate can be loaded into the GeneTitan™ MC

Instrument.

Using the automated target preparation protocol, workﬂows are available for processing 8 array plates

per work week, or 3 array plates per week.

•Chapter 6, “8-plate workﬂow for CytoScan™ HT-CMA Array Plates”

•Chapter 7, “3-plate workﬂow for CytoScan™ HT-CMA Array Plates with a 3-hour DNA precipitation

step”

•Chapter 8, “3-plate workﬂow for CytoScan™ HT-CMA Array Plates with an overnight DNA

precipitation step”

Chapter 1 Overview

Multiplate workﬂows

1

12 CytoScan™ HT-CMA Assay 96-Array Format Automated Workﬂow User Guide—Applied Biosystems™ NIMBUS™ Instrument

Overview of the CytoScan™ HT-CMA Assay 96-Array Format

Automated Workﬂow on the NIMBUS™ Instrument

Genomic DNA preparation

Day 1 Chapter 2, Genomic DNA preparation

▼

Target preparation

Day 1 Stage 1: Amplify the genomic DNA

(NIMBUS™ Instrument)

▼

23 ± 1-hour ampliﬁcation at 37°C.

Optional stopping point.

Day 2 Stage 2: Fragment and precipitate the DNA

(NIMBUS™ Instrument)

▼

Approximate time: 16—24 hours (or optional

3‑hour precipitation step) –20°C incubation of

Precipitation Plate

Day 3 Stage 3: Centrifuge and dry pellets

(O-deck)

▼

Optional stopping point.

Day 3 Stage 4A and 4B: Resuspension and hybridization

preparation

Stage 4C: Perform sample QC

(NIMBUS™ Instrument and o-deck)

▼

Stage 4C:

Optional stopping point.

Day 3 Stage 5: Prepare the hybridization tray

(NIMBUS™ Instrument)

▼

Day 3 Denature the hybridization-ready samples

(NIMBUS™ Instrument and o-deck)

▼

23.5- to 24-hour array hybridization in the

GeneTitan™ MC Instrument.

Day 4 Stage 6: Prepare GeneTitan™ reagent plates

(NIMBUS™ Instrument)

Array processing

Day 5 Chapter 5, Process array plates with the GeneTitan™

Multi-Channel (MC) Instrument

Array processing is completed with the GeneTitan™

MC Instrument and GeneChip™ Command Console™

software v4.3 or later.

Fluidics: 5 hours

Scan: ~7.5 hours

Chapter 1 Overview

Overview of the CytoScan™ HT-CMA Assay 96-Array Format Automated Workﬂow on the NIMBUS™ Instrument 1

CytoScan™ HT-CMA Assay 96-Array Format Automated Workﬂow User Guide—Applied Biosystems™ NIMBUS™ Instrument 13

Genomic DNA preparation

■Sources of genomic DNA .............................................................. 14

■General requirements ................................................................. 15

■Genomic DNA extraction and puriﬁcation methods ....................................... 17

■Genomic DNA cleanup ................................................................ 18

■Genomic DNA preparation ............................................................. 18

■GeneTitan™ Array Plate Registration ﬁle ................................................. 21

The general requirements for genomic DNA (gDNA) sources and extraction methods are described

in this chapter. The success of this assay requires uniform ampliﬁcation of the genome starting with

relatively intact gDNA. To achieve uniform ampliﬁcation, the gDNA must be of high quality, and must be

free of contaminants that can aect the enzymatic reactions to be performed.

For this protocol, you use the Applied Biosystems™ HT Target Prep Reagent Kit 96F (Cat. No. 906024).

Genomic DNA Standard (Ref 103) (Cat. No. 951957), available separately, meets the DNA requirements

that are outlined in this chapter and can be used as a control. The size and purity of sample gDNA can

be compared with the size and purity of the control DNA to evaluate sample quality. Routinely use the

control DNA as an experimental positive control and for troubleshooting purposes.

Assay performance can vary for gDNA samples that do not meet the general requirements. However,

the reliability of any given result must be evaluated in the context of overall experimental design and

goals.

Sources of genomic DNA

The following sources of human gDNA have been successfully tested in the laboratories at Thermo

Fisher Scientiﬁc for DNA that meets the requirements for the CytoScan™ HT-CMA Assay.

•Whole blood

•Cell lines

•Amniotic ﬂuid

Other sample types have not been veriﬁed in this assay and are not currently supported.

Note: DNA derived from formalin‑ﬁxed paran-embedded (FFPE) blocks must not be used with this

assay.

2

14 CytoScan™ HT-CMA Assay 96-Array Format Automated Workﬂow User Guide—Applied Biosystems™ NIMBUS™ Instrument

General requirements

•Starting DNA must be double-stranded for accurate concentration determination.

•DNA must be of high purity. DNA must be free of DNA polymerase inhibitors. Examples of inhibitors

include high concentrations of heme (from blood) and high concentrations of chelating agents

(that is, EDTA). The gDNA extraction and puriﬁcation method must create DNA that is salt-free,

because high concentrations of particular salts can inhibit enzyme reactions. DNA purity indicated

by OD260/OD280 and OD260/OD230 ratios. The OD260/OD280 ratio should be between 1.8 and 2.0

and the OD260/OD230 ratio should be greater than 1.5. We recommend that DNA samples that do

not meet these criteria be cleaned up as described in “Genomic DNA cleanup” on page 18.

•DNA must not be degraded. The average size of gDNA can be evaluated on a 1% agarose gel

using an appropriate size standard control. Approximately 90% of the DNA must be greater than

10 Kb in size. Control DNA can be run on the same gel for comparison.

•IMPORTANT! We recommend that the assay plate contain at least 90 samples for accurate

determination of SMN1 carrier status on the CytoScan™ HT-CMA 96-Array Plate. For questions

regarding this recommendation contact Thermo Fisher Scientiﬁc technical support.

Note: DNA size integrity is important for successful assay performance. We recommend evaluating

gDNA by gel electrophoresis.

Special requirements

Preampliﬁcation area

Precautions are required when manipulating genomic DNA to avoid contamination with foreign DNA

ampliﬁed in other reactions and procedures. It is recommended that genomic DNA manipulations are

performed in a dedicated preampliﬁcation room or area separate from the main laboratory.

This preampliﬁcation area requires a dedicated set of pipettes and plasticware. If no dedicated area is

available, use of a dedicated bench or a dedicated biosafety hood and dedicated pipettes is suggested.

If no dedicated bench or biosafety hood is available, a set of dedicated pipettes is recommended.

Chapter 2 Genomic DNA preparation

General requirements 2

CytoScan™ HT-CMA Assay 96-Array Format Automated Workﬂow User Guide—Applied Biosystems™ NIMBUS™ Instrument 15

Evaluate the quality of genomic DNA with 1% agarose E‑Gel™

We recommend this quality control step to evaluate the quality of the gDNA before starting the assay.

Equipment and reagents required

Item Source

Invitrogen™ Mother E-Base™ Device EBM03

Invitrogen™ Daughter E-Base™ Device (optional for running multiple gels in parallel) EBD03

Invitrogen™ E‑Gel™ 48 Agarose Gels, 1% G800801

Invitrogen™ RediLoad™ Loading Buer 750026

Invitrogen™ E‑Gel™ 96 High Range DNA Marker 12352019

Guidelines for gDNA Sample Plate preparation

The following guidelines are recommended when preparing the gDNA Sample Plate for gel analysis.

•Loading a DNA mass of 10 ng to 20 ng per well is recommended. If lower amounts are loaded,

omission of the loading dye is recommended to improve visualization. Loading ≥25 ng gDNA per

well can improve the image.

•Add 3 µL of 0.1X of RediLoad™ Loading Buer (RediLoad™ Loading Buer dye diluted 10-fold with

nuclease-free water) dye to each sample.

•Bring each sample to a total volume of 20 µL using nuclease-free water. For example, if the volume

of genomic DNA is 5 µL, add 3 µL of RediLoad™ Loading Buer, and bring to 20 µL total by adding

12 µL of water.

•Seal, vortex, and centrifuge brieﬂy.

Run a 48-lane 1% agarose E‑Gel™

1. Power on the E-Base™ device (red light).

2. Push Power/Prg to ensure that the gel base is in EG mode, not EP mode.

3. Insert the E‑Gel™ 48 Agarose Gels, 1% into the slot.

4. Remove 2 combs.

5. Load 20 µL of gDNA samples onto the E‑Gel™ 48 Agarose Gels, 1%.

6. If needed, load 15 µL of diluted E‑Gel™ 96 High Range DNA Marker (1:3 dilution or ~0.34X from

stock) into all marker wells.

7. Fill all empty wells with water.

Chapter 2 Genomic DNA preparation

General requirements

2

16 CytoScan™ HT-CMA Assay 96-Array Format Automated Workﬂow User Guide—Applied Biosystems™ NIMBUS™ Instrument

8. Adjust the run time to ~27 minutes.

9. Push Power/Prg again.

It changes from red to green.

When run time is reached (the ladder band reaches the end of the lane), the system automatically shuts

o. The gel is ready for imaging.

E‑Gel™ results

The following ﬁgure shows gel images of intact gDNA (that is appropriate for use in the CytoScan™

HT-CMA Assay) and degraded gDNA samples. For gDNA that is degraded, perform a test experiment

to investigate the performance of their samples in the CytoScan™ HT-CMA Assay before starting any

large-scale genotyping projects.

10 kb

2 kb

4 kb

0.8 kb

0.4 kb

1 2

Figure 1 Gel images with intact gDNA and degraded gDNA

1Intact samples 2Degraded samples

Genomic DNA extraction and puriﬁcation methods

Genomic DNA extraction and puriﬁcation methods that meet the general requirements that are outlined

are expected to yield successful results. Methods that include boiling or strong denaturants are

not acceptable because the DNA would be made single-stranded and can no longer be accurately

quantiﬁed using a PicoGreen™-based assay.

Chapter 2 Genomic DNA preparation

Genomic DNA extraction and puriﬁcation methods 2

CytoScan™ HT-CMA Assay 96-Array Format Automated Workﬂow User Guide—Applied Biosystems™ NIMBUS™ Instrument 17

Genomic DNA cleanup

If a gDNA preparation is suspected to contain inhibitors, the following cleanup procedure can be used.

1. Add 0.5 volumes of 7.5 M NH4OAc, 2.5 volumes of absolute ethanol (stored at −20°C), to gDNA.

2. Vortex, then incubate at −20°C for 1 hour.

3. Centrifuge at 12,000 × g in a microcentrifuge at room temperature for 20 minutes.

4. Remove supernatant, then wash pellet with 80% ethanol.

5. Centrifuge at 12,000 × g at room temperature for 5 minutes.

6. Remove the 80% ethanol, then repeat the 80% ethanol wash one more time.

7. Resuspend the pellet in Low EDTA TE Buer (10-mM Tris-HCl pH 8.0, 0.1 mM EDTA).

Genomic DNA preparation

This step must be done before proceeding with the DNA ampliﬁcation stages.

The genomic DNA (gDNA) you process using the CytoScan™ HT-CMA Assay must meet the general

requirements that are listed earlier in this chapter. The amount of gDNA is 100 ng for the CytoScan™

HT‑CMA whole-genome ampliﬁcation step.

Genomic DNA input requirements

Sample type Volume per well Input mass

per well

gDNA

concentration

Stage 1: DNA ampliﬁcation 20 µL 100 ng 5 ng/μL

Time required

Allow 30–60 minutes for reagents to thaw and 30 minutes for setup.

Chapter 2 Genomic DNA preparation

Genomic DNA cleanup

2

18 CytoScan™ HT-CMA Assay 96-Array Format Automated Workﬂow User Guide—Applied Biosystems™ NIMBUS™ Instrument

Equipment, consumables, and reagents required

Unless otherwise indicated, all materials are available through thermoﬁsher.com.

Equipment and consumables required

Quantity Item

As required Adhesive seals for plates

1 Ice bucket, ﬁlled with ice

1 each Pipettes: single channel P10 or P20

Optional: multichannel P10 or P20

As required Pipette tips

1 Round deepwell plate, one of the following:

•Axygen™ 96-well Round Deepwell Plate (sterile, PDW20CS), Fisher Scientiﬁc™,

14-222-354.

•Axygen™ 96-well Round Deepwell Plate (nonsterile, PDW20C), Fisher Scientiﬁc™,

14-222-353.

•PerkinElmer™ Deepwell StorPlate-96 U Round, 2.0mL (6008490 only), Fisher

Scientiﬁc™, 50-905-1741.

1 96‑well PCR plate, one of the following:

•Bio-Rad™ HSS9641 (green) or HSS9601 (clear) for Applied Biosystems™

GeneAmp™ PCR System 9700, Applied Biosystems™ Veriti™ Thermal Cycler, and

Applied Biosystems™ ProFlex™ PCR System

•Bio-Rad™ HSS9641 (green) or HSS9601 (clear) for the Eppendorf™ Mastercycler™

pro S

1 Plate centrifuge

1 Plate spectrophotometer (required only if no OD measurements available for samples)

1 Vortexer

Reagents required

Reagent Source

Genomic DNA Standard (Ref 103), 10 ng/µL 951957

Reduced EDTA TE Buer (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA) Fisher

Scientiﬁc™,

AAJ75793AE

Quant-iT™ PicoGreen™ dsDNA Assay Kit P7589

Chapter 2 Genomic DNA preparation

Genomic DNA preparation 2

CytoScan™ HT-CMA Assay 96-Array Format Automated Workﬂow User Guide—Applied Biosystems™ NIMBUS™ Instrument 19

Thaw samples and control

Thaw the following components to room temperature:

• gDNA samples

• Genomic DNA Standard (Ref 103)

To thaw, either:

•Place items on benchtop for 60 minutes.

•Thaw in a water bath.

a. Fill a small plastic dish with ultra-pure water. Do not overﬁll to prevent the level of the water

overﬂowing when the sample tubes or plates are placed in the bath.

b. Thaw the sealed gDNA Sample Plate and control DNA tubes for 30 minutes.

c. Remove the gDNA Sample Plate and/or the control DNA tube from the water bath and wipe

dry using laboratory wipes. Ensure that the outside is dry before opening the gDNA Sample

Plate or tube to minimize any contamination, which can lead to reaction failure.

Quantify and dilute test sample gDNA

1. Gently vortex (50% maximum), then centrifuge the gDNA samples and Genomic DNA Standard

(Ref 103).

2. Recommendation: Quantify each sample (for example, using the Quant-iT™ PicoGreen™ dsDNA

Assay Kit).

3. Using Low EDTA TE Buer, dilute each sample to a concentration of 5 ng/µL.

4. Seal, vortex, then centrifuge.

Note: Do not dilute the Genomic DNA Standard (Ref 103). It is already at a working concentration.

Note: We recommend that you determine the sample concentrations using the Quant-iT™ PicoGreen™

dsDNA Assay Kit (Cat. No. P7589). Sample concentration that is determined by UV absorbance is often

inaccurate and can yield dierent results.

Aliquot diluted samples and the Genomic DNA Standard (Ref 103) control to

the deepwell plate

1. Aliquot 20 µL of each diluted gDNA sample to all 96 wells in the round deepwell plate.

2. Pipet 20 µL of Genomic DNA Standard (Ref 103) control.

We recommend including at least 1 positive control on each plate.

3. Seal, then centrifuge.

Chapter 2 Genomic DNA preparation

Genomic DNA preparation

2

20 CytoScan™ HT-CMA Assay 96-Array Format Automated Workﬂow User Guide—Applied Biosystems™ NIMBUS™ Instrument

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Thermo Fisher Scientific CytoScan HT-CMA Assay 96-Array Format Automated Workflow User guide

Thermo Fisher Scientific CytoScan HT-CMA Assay 96-Array Format Automated Workflow User guide

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