GenetiSure Dx Postnatal Assay - PowerPoint Presentation

Slide1

GenetiSure Dx Postnatal Assay

Improving Quality of Life

For In Vitro Diagnostic Use Available only in EU

Slide2

Why CGH array in postnatal genetic testing?

GenetiSureDx

Postnatal Assay

Clinical performances – results you can trust

CytoDx Resolving the analysis bottleneck

Support

Ordering information

Summary & contacts

For In Vitro Diagnostic Use Available only in EU

Slide3

Why CGH array in postnatal genetic testing?

The genetic disease landscape

A definitive g

enetic diagnosis provides the cause of disease and changes the focus of a medical investigation to appropriate medical care.

Our focus: Improving quality of life

Genetic anomalies account for

25-50%

of ID cases

(this number increases with the severity of the disability)

Copy number changes

cause

~25 to 30%

of all major congenital dysmorphisms

At least 10%

of all neonatal intensive care unit admissions report congenital dysmorphismsMedian global prevalence of ASD alone was an estimated

62/10,000 in 2012

For In Vitro Diagnostic Use Available only in EU

Slide4

Why CGH array in postnatal genetic testing?

With higher diagnostic yield,

increased resolution

and

greater sensitivity, aCGH is a superior analysis method, especially when compared to traditional karyotyping or FISH. Medical geneticists now consider aCGH to be the standard test for detecting CNVs linked to a unique patient

Our fully established protocols can detect Copy number and copy neutral aberrations in a single experiment resulting in

workflow stability, robustness, time to result and easiness of data analysis. This makes aCGH is the preferred solution for routine diagnostics when compared to NGS.

For In Vitro Diagnostic Use Available only in EU

Slide5

Microarrays are a proven technology used in hundreds of laboratories around the world. Agilent aCGH arrays have established a standard of excellence for the characterization of genetic diseases with more than

10 years of research use and more than 10,000 published papers.

aCGH

is recognized

as the first-tier test for diagnosis of genetic anomalies associated with developmental disabilities

by:

the American College of Medical Genetics (ACMG)

Childhood Neurology Society

the American Academy of Neurology (AAN)

Why CGH array in postnatal genetic testing?

The following entities have established guidelines for array-based whole genome

“

molecular karyotyping” in constitutional genetic diagnosis :European Society of Human Genetics (ESHG)

European Cytogeneticists Association

Canadian College of Medical GeneticistsHuman Genetics Society of AustralasiaFor In Vitro Diagnostic Use Available only in EU

Slide6

Not just an array…A complete workflow, from DNA to results

Hybridization oven and chambers are general lab equipment and can be purchased separately

GenetiSure Dx Postnatal Array

GenetiSure Dx

Reagents

SureScan Dx

CytoDx GenetiSure Dx Postnatal Assay

For In Vitro Diagnostic Use Available only in EU

Slide7

GenetiSure Dx Postnatal Assay

Designed for what matters

GenetiSure Dx Postnatal Array is designed to allow

the

identification of copy number and copy neutral changes across the entire genome

.

Each microarray contains approximately: 107,000 probes optimized for copy number (CN) analysis 59,000 bi-allelic SNP probes  

For In Vitro Diagnostic Use Available only in EU

Slide8

GenetiSure Dx Postnatal Assay

 

High Assay Resolution

Confidently call CNs with as low as 5 consecutive probes

The probes are targeting overall 94% of the genome with at least 5 CN probes per 400 kb

Median resolution is approximately:

25 Kb for clinically relevant regions

150 kb genome wide8Mb for LOH

The SNP probes target 91% of the genome, with at least 100 SNP probes

per 10 MbDetect mosaic amplifications and deletions spanning 20 or more probes

For In Vitro Diagnostic Use Available only in EU

Slide9

GenetiSure Dx Postnatal Assay

 

Genetisure Dx processing reagents

Labeling, Hybridization and washing

reagents are validated for diagnostic

and optimized for use with GenetiSure Dx Array

Dedicated reagents allow streamlined sample processing Only 500 ng of genomic DNA are required for testing, (extracted from 200 μl of whole blood)The accuracy of the GenetiSure Dx

Postnatal Assay results is not affected by increased levels of hemoglobin, conjugated bilirubin, unconjugated bilirubin or triglycerides in the patient’s whole blood in EDTA, or by storage of the blood for up to seven days.

For In Vitro Diagnostic Use Available only in EU

Slide10

GenetiSure Dx Postnatal Assay

Data Generation - Outstanding sensitivity and resolution

The

SureScan Dx Microarray Scanner

is the foundation of our GenetiSure Dx Postnatal Assay that offers outstanding sensitivity and resolution, delivering flexibility to analyze genomics and cytogenetics microarrays.

Easy data Interpretation with quality data and crisp images from high resolution scans

Streamlined workflow with continuous slide loading capability to allow 24/7 lab operations Full integration of data analysis software for a seamless workflow Manufactured under ISO 13485 certificationsThe Agilent SureScan Dx Microarray Scanner is CE marked for in vitro diagnostic use in the Europe Union, Iceland, Korea, Norway, Singapore, and Switzerland.

For In Vitro Diagnostic Use Available only in EU

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Easy laboratory set up

Magnetic stir plates

Microcentrifuge

Pipettes on rack

Water bath or incubator

Fluorometer Nanodrop Vacuum concentrator Centrifuge Hyb oven Surecycler SureScan Dx Freezer

Refrigerator Ice bucket Vortex mixer

less lab space required, for easier implementation No pre-post PCR room (area) required Less capital investment to complete lab equipment X

Workflow optimized for the laboratory

For In Vitro Diagnostic Use Available only in EU

Slide12

3 hours

3.5 hours

1.5 hours

2 hours

24 hours

0.5 hours16min/slide

Easy and streamlined protocol The assay is comprehensive and easy to implement to the laboratory routine. Time to result, including data analysis, is 3 days. The whole protocol requires less than 4h hands on time

Image acquisition is completely automated thanks to with

automatic calibration and autofocus capabilities Workflow optimized for the laboratory For In Vitro Diagnostic Use Available only in EU

Slide13

Built-in quality controls

The Genetisure Postnatal Dx Assay includes a series of in-process QC checks that allow the user to easily monitor and assess the quality of results.

The controls include:

Validated reference DNA

Array QC metrics

Workflow QC checkpoint

Workflow optimized for the laboratory For In Vitro Diagnostic Use Available only in EU

Slide14

Reproducibility

precision

Whole blood stability

Results you can trust

Clinical validity

Accuracy

Limit of detection

Validation studies performed on the Assay

Clinical performances – results you can trust

The GenetiSure Dx Postnatal assay has been validated with a Clinical study involving different partner laboratories, and including more than 900 samples.

During the study we obtained a diagnostic yield of 15% and 92.9% agreement with the reference diagnosis for Copy Number.

Interfering substance

Cross- contamination

For In Vitro Diagnostic Use Available only in EU

Slide15

This is an example of 1.6 Mb gain covered by 88 probes detected at

Chr

7q11.23.

The patient underwent genetic testing because of an indication of developmental delays and autism symptoms.

The reported aberration suggested a microduplication syndrome.

Sample reporting an 17 Kb deletion at Chr. 16p13.3 covered by 12 CGH probes.

The deleted region spans two HBA genes, which can be easily identified by the Gene track in CytoDx.

The findings are consistent with patient clinical indication reporting an

alloimmunization

history and

Hirschsprung-like symptoms. Example of clinical samples reporting gain and loss Clinical performances – results you can trust

For In Vitro Diagnostic Use Available only in EU

Slide16

A deletion event is confirmed by both CGH and SNP probes.

Figure illustrates how the Agilent ADM-2 algorithm calls a larger 4.3 hemizygous deletion on the p arm of chromosome 8, spanning 186 CGH probes.

The LOH calling algorithm shows that in the same region there are only single A or B SNP alleles (0 or 1 uncut) instead of the combination of AA, AB, and BB SNP alleles (0, 1, and 2 uncut alleles) present in a normal diploid genome.

Example of clinical samples reporting gain and loss

Clinical performances – results you can trust

CGH

LOH

For In Vitro Diagnostic Use Available only in EU

Slide17

Copy neutral loss of heterozygosity is also detectable using the Agilent

aCGH

assay. For each SNP probe, gDNA that has been cut at the restriction site results in a different fluorescent signal than that produced by uncut gDNA. Genotyping of SNPs allows for subsequent detection of cnLOH intervals, identified in the software by locating genomic regions with a statistically significant scarcity of heterozygous calls.

This is an example of a 10.5 Mb cnLOH at Chr. 15q26.1- q26.3. Also visible is an additional small LOH region close to centromere

AOH at centromere and telomere is consistent with UPD due to MII nondisjunction.

Findings are consistent with the clinical phenotype of

Prader

-Willi syndrome. Additional methylation tests are required for validation.

Example of clinical samples reporting LOH Clinical performances – results you can trust

For In Vitro Diagnostic Use Available only in EU

Slide18

Down syndrome (DS) is one of the most frequent congenital birth defects and genetic cause of mental retardation.

The reason for referral of this patient was Tetralogy of

Fallot

with Absent Pulmonary Valve.

Trisomy of Chr. 21 is highlighted both from copy number and SNP probes

A sample reporting a 29 Mb amplification at 21q11.2-q22.3 and a 4.5 Mb deletion at 21q22.3.

This aberration is suggestive of a ring chromosome resulting in a partial for Chr. 21, later confirmed by karyotype Example of clinical samples reporting whole chromosome aberration

Clinical performances – results you can trust

For In Vitro Diagnostic Use Available only in EU

Slide19

Home Tab with Useful Features

Streamlined workflow for data analysis with full automation of data upload and analysis

Cyto

Dx resolving the analysis bottleneck

For In Vitro Diagnostic Use Available only in EU

Slide20

Manual Processing with Easy 3-step Workflow

Cyto

Dx resolving the analysis bottleneck

For In Vitro Diagnostic Use Available only in EU

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Automated Processing

Start from Home screen

Follow

status

Cyto

Dx resolving the analysis bottleneck

For In Vitro Diagnostic Use Available only in EU

Slide22

Genome

viewer

Left:

Chromosome

viewer with CGH and SNP panelsRight: Gene &Track viewer

Aberrations

Table Viewer Link out to external databasesAdd classification to intervals

SelectedTracks

Suppress reporting of aberrationsFull audit trail

Access to sample’s QC metrics

Modify/edit callsCytoDx:

Superior Graphical Displays to Visualize and Triage the Results in an Intuitive Way

For In Vitro Diagnostic Use Available only in EU

Slide23

Actionable and Informational QC Metrics, Giving Users Confidence in Their Assay Results

Failsafe:

Cyto

Dx prevents user from signing off on sample if any QC metrics in Actionable category failCyto

Dx resolving the analysis bottleneck For In Vitro Diagnostic Use Available only in EU

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Generate a Variety of Reports with Robust Reporting Tool

Cyto

Dx resolving the analysis bottleneck

For In Vitro Diagnostic Use Available only in EU

Slide25

Flexible User Roles Management

There are 4 user roles in CytoDx.

System Admins

are responsible for installing the software, administering user functions, and configuring the software. They can also view activity logs and audit trails.

 Technicians have very limited access; they can only run workflows on sample files. 

Cytogeneticists can run workflows as well and they can also check out the sample results, which means that they can annotate the results. Additionally, they can generate pre-final reports and view audit trails.

 Lab Directors are mainly responsible for reviewing sample results and ultimately signing off on those results.CytoDx resolving the analysis bottleneck

For In Vitro Diagnostic Use Available only in EU

Slide26

System Requirements for Agilent CytoDx Computers

Requirements for computers running CytoDx Server:

Operating system 64-bit Windows 7 Enterprise or Windows 10 Enterprise

CPU: Intel Core i7 or better

RAM: 8 GB or betterDisk: 2 TB.Display 1280 x 768 or betterAny program for opening PDF files (for example, Adobe Reader)Requirements for computers running CytoDx Client:Operating system 64-bit Windows 7 Enterprise or Windows 10 EnterpriseCPU: Intel Core i7 or betterRAM: 8 GB or betterDisk 500 GB.Display 1280 x 768 or betterAny program for opening PDF files (for example, Adobe Reader)

CytoDx Server and Client can be installed on the same machine or on different machines

CytoDx resolving the analysis bottleneck For In Vitro Diagnostic Use Available only in EU

Slide27

Software Summary

Excellent Solution for Clinical Postnatal Labs

Streamlined workflow for data analysis with full automation of data upload and analysis

Flexible user management

Fully customizable Cyto reportTutorial videos available in the SWComplete audit trail recording for maximum traceability

Superior Visual Tools to visualize and triage the results in an intuitive way.Array-level QC metrics that are grouped into

Actionable and Informational categories, giving users confidence in their assay results.Robust Algorithm for Data Analysis.Validated algorithms for analysis of the Agilent GenetiSure Dx Postnatal CGH+SNP Microarray data, which identify both copy number variations (CNV) and copy-neutral losses of heterozygosity (

cnLOH) with high confidence and accuracy, all in one array

Convenient Tools for Data Interpretation.Various useful tracksLinks to external databases

CytoDx resolving the analysis bottleneck

For In Vitro Diagnostic Use Available only in EU

Slide28

Bioinformatics

Agilent is the only company able to provide both Data Analysis and Data interpretation software

CytoDx has been developed and validated for GenetiSure Assay.

Bench can analyze CGH data and integrate them with NGS,

Bench

is classified as Medical device Class I in Europe

For In Vitro Diagnostic Use Available only in EU

Slide29

Dedicated support

Agilent support provides:

Dedicated email and phone line for diagnostic customers

A team of multilingual field application scientists

Training tailored on customer needs for streamlined adoption of the technology

Agilent experience and quality support

For In Vitro Diagnostic Use Available only in EU

Slide30

Ordering information

For In Vitro Diagnostic Use Available only in EU

BUNDLE including all reagents for 24 or 48 reactions available soon

K1202B – 24 reaction

K1202C – 48 reaction

* Oven and hyb chamber are general lab equipments, do not require Dx marking

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Based on Agilent OLS technology, producing high quality oligo 60mer long

Only protocol providing a real comparative analysis, with reference and sample co-hybridized on same array

no DNA amplification required in the protocol, limiting contamination risk and allowing to better discriminate copy number information

Data analysis software with preloaded validated protocols for sample processing

Fully validated for use in postnatal diagnostic, marked.

For In Vitro Diagnostic Use Available only in EU

Slide32

Intended Use

GenetiSure

Dx

Postnatal Assay is a qualitative assay intended for the postnatal detection of copy number variations (CNV) and copy-neutral loss of heterozygosity (

cnLOH) in genomic DNA obtained from peripheral whole blood in patients referred for chromosomal testing based on clinical presentation. GenetiSure

Dx Postnatal Assay is intended for the detection of CNVs and cnLOH associated with developmental delay, intellectual disability, congenital anomalies, or dysmorphic features. Assay results are intended to be used in conjunction with other clinical and diagnostic findings, consistent with professional standards of practice, including confirmation by alternative methods, parental evaluation, clinical genetic evaluation, and counseling, as appropriate. Interpretation of assay results is intended to be performed only by healthcare professionals, who are board-certified in clinical cytogenetics or molecular genetics. The assay is intended to be used on the SureScan

Dx Microarray Scanner System and analyzed by CytoDx Software. This device is not intended to be used for standalone diagnostic purposes, preimplantation or prenatal testing or screening, population screening, or for the detection of, or screening for, acquired or somatic genetic aberrationsFor In Vitro Diagnostic Use Available only in EU