DESKTOP GENETICSSITE-SEQ

CONFIDENTLY VALIDATE CRISPR EXPERIMENTS

Desktop Genetics makes it easier for researchers to use CRISPR genome editing to confidently validate genotype-to-phenotype associations.

Our Site-Seq service combines targeted amplicon sequencing with internal bioinformatics expertise for accurate validation of on- and off-target genome editing outcomes.

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TECHNIQUESEQUENCE

DATADETECTION

LIMITADVANTAGE DISADVANTAGE

Mismatch Cleavage

No 5%1 Quick, Simple, Cost-effectiveLimited sensitivity, Unsuitable

for high-throughput investigations

Sanger Sequencing

Yes 20%2 Cost-effective in low-throughput investigations

Limited sensitivity, Unsuitable for heterogenous populations

Targeted Amplicon Sequencing

Yes 0.01%3 Sensitive, High-throughputCost-prohibitive for

low-throughput investigations

INVESTIGATING EDITING OUTCOMES

CRISPR ACTIVITY AND SPECIFICITY

DESKTOP GENETICS SITE-SEQOur Site-Seq™ service incorporates targeted amplicon sequencing to carry out deep

sequencing and analysis of PCR products (amplicons) for identifying CRISPR mutations.

Site-Seq™ is a rapid and robust service for confidently validating the efficiency and

distribution of CRISPR mutations at on- and off-target sites. This service enables quantitative

assessment of genome modification and facilitates the reproducibility of CRISPR research.

Common techniques for validating CRISPR experiments include mismatch cleavage assays

(e.g. T7E1, Surveyor, RFLP, etc.) and Sanger sequencing. Although both approaches are

cost-effective and easy methods for detecting edited DNA, they lack the sensitivity to detect

minor allele frequencies and are better suited to low-throughput investigations.

Comparatively, targeted amplicon sequencing provides a high-throughput option for reliably

detecting editing events at frequencies as low as 0.01%.

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OVERVIEW OF CRISPR DETECTION ASSAYS

1Vouillot et al. 2015, 2Davidson et al. 2012, 3Hendel et al. 2015

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ACTIVITY AND SPECIFICITY ANALYSIS

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SAMPLE SITE-SEQ REPORT

Analysis Overview

After running your samples through our NGS pipeline, we will perform a comprehensive analysis on the data and provide you with a visual activity summary report with data on:

● Editing efficiency○ SNP/Indel size○ SNP/Indel frequency○ SNP/Indel identity○ Predicted Effect on Translation

Pipeline Overview

● Paired-end input FASTQ file reads are stitched and filtered. In our example data set:

○ 119,710 FASTQ reads were stitched○ 119,024 high quality reads were used for

SNP/Indel profiling○ 671* individual SNP/Indel profiles

identified by pairwise alignment

*Note: SNP/Indel profiles should be present in at least 2 high-quality reads

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SITE-SEQ SERVICE

STANDARD SERVICE PARAMETERS

Detection NHEJ/HDR

Input Material Min. 50 ng gDNA

Coverage 5000x

Read Length 150 bp Paired-End

Species Available Over 20 incl. Human, Mouse, Rat, Zebrafish, Worm, Fruit Fly

Amplicon Design Primer Design Up to 250 bp

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PRICING

SPECIFICATIONS

NUMBER OF SAMPLES STANDARD PRICING

10 – 16 Samples $125/sample

17 – 48 Samples $115/sample

49 – 96 Samples $100/sample

Special Launch Offer

First 50 customers

$95/sample (min. 10 samples)

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HOW TO ORDER SITE-SEQ

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DNA TO DATA IN 25 WORKING DAYS

PERFORM CRISPR EXPERIMENT EMAIL NGS@DESKGEN.COM

SEND EXPERIMENTAL SAMPLES

SAMPLES SEQUENCED

DATA ANALYZED

REPORT GENERATED

DELIVERED TO YOU

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FREQUENTLY ASKED QUESTIONS

Yes. Site-Seq™ can be used for targeted amplicon sequencing and analysis of on-target

CRISPR activity. This can be used to determine editing efficiency and frequency in knockout

and knockin CRISPR applications.

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Yes. Site-Seq™ can be used for detecting off-target CRISPR activity. Provide us with the list of

your predicted off-target sites and we will carry out sequencing and analysis for each target

site.

CAN I REQUEST A FASTER TURNAROUND TIME?

Yes. Site-Seq™ can be ordered for low-throughput projects. Customers requiring sequencing

and analysis of less than 10 samples can order Site-Seq at a fixed price of  $1,250.

Yes. Site-Seq™ has a standard turnaround time of 25 working days from receipt of your

genomic DNA. However, customers who pre-pay can request an expedited 10 working day

turnaround time. We also offer a 25% credit on next purchase if we miss our deadline.

CAN I ORDER SITE-SEQ FOR <10 SAMPLES?™

CAN I USE SITE-SEQ FOR ON-TARGET ACTIVITY?™

CAN I USE SITE-SEQ FOR OFF-TARGET ACTIVITY?™