Causes of copy number variation

Identification of copy number variation

Consequences of copy number variation

Importance of copy number variation

Background

Analyzing the results

Camouflage regions of the genome

Type of CNV

CNV Quality Scores

Data used to call CNVs

Investigating CNVs in more detail

CNV visualization

CNV Plots

Conclusion

What is Myopic Choroidal Neovascularization

Symptoms of Myopic CNV

What is Myopic CNV?

Diagnosis

Treatments for Myopic Choroidal Neovascularization

Conclusion

What are copy number variations?

How to detect copy number variation with digital PCR

CNV quantification

Sample Prep

Measuring Tandem Copies

How to interpret digital PCR data

Conclusion

Structural Variation

Cmvs

Detect It Using Genotype Data

The Log Ratio

Plink To Analyze the Cnb Data

Cnb Map File

What Does Cnb Analysis Output Look like

Run Cnb Association Tests at Individual Cmb Loci or at Individual Break Points of Cnbs

Considerations

Multiple Testing Correction

Introduction

QIAseq FX Single Cell DNA Library Kit

High and Even Genomic Coverage

High Fidelity and Low Error Rate

Detection of Sub-Chromosomal Copy Number Variations

Conclusions

Today's Attendance URL and QR code

Where to begin?

Next step: Assessing the genes within the CNV

What if the phenotype isn't consistent (4D)?

Segregation In Affected Family Members

Segregation Example: AD Hypertrophic Cardiomyopathy

Overlap with Established TS, HI, or Benign Genes/Genomic Regions

Other cases: Padiath et al. 2006

What about the rest of the cases?

Summary

Agenda

Detecting small CNV events

CNV analysis example

Reference samples

Heterozygous single exon deletion

Editing CNV information

Tuning between sensitivity and specificity

View CNV events

How many samples are required to build a reference set?

Conclusion

Webinar Objectives

Correlation with genotype

Creating a Cluster File

Calculating VCF

Copy Neutral Loss of Heterozygosity (CNH)

GenomeStudio Requirements

FAN-B Analysis

Import data into BlueFuse

Importing Data Manually

Q&A session

Welcome

Attendance URL and QR Code

Uncoupling Variant Classification from Clinical Significance

Section I: Initial Assessment of Genomic Content

Established CNV regions

CNV Calculator Tool

What does this mean for our case?

Documenting your decisions

How to report new information

Conclusion

Introduction

Clinical CNV Application

Registration Methodology

Electrode Application

CNV Registration

Results Analysis

Chromosome microarray test

What is a copy number variant?

Understanding genetic test results

Consequences of CNV

Conclusion

Intro

Maximizing Sequencing Efficiency

Competitor exome data

The learning loop

Challenges

Detecting copy number variations

Long-range and short-range events

What are the benefits of this partnership?

Q&A: Do you follow standard VCF formatting for reporting CNV calling?

Conclusion

Microarray

Results

Interpretation

The Chromium Single Cell CNV Solution

10x Software Tools

Reagents in Solution

In the Chromium Controller - Stage 1

In the Chromium Controller - Stage 2

Welcome

Target Panel Design

High-level amplification example

Data Processing

Summary

Segment Metrics

Scatter Plots

Focal deletion detection

Can we use CMNexus for exon-level copy calling?

Conclusion