Unique software tools to increase accuracy & speed of DNA Variant Detection

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1 Unique software tools to increase accuracy & speed of DNA Variant Detection SoftGenetics Technology performs physical comparison of DNA sequence traces providing High sensitivity, accuracy to >99% and reliability to discover Homozygote Heterozygote Indels SoftGenetics,Inc.

2 Mutation Explorer Software for Detecting SNPs and Mutations from DNA Sequence Traces Mutation Explorer is a software package specifically designed for detecting SNP and mutations from DNA sequence traces, created from either slab gel or capillary electrophoresis. The software compares the sequence traces of mutant samples to the wildtype reference. It detects homozygous, heterozygous and insertions/deletions. All of the mutations are represented as sharp peaks, which are distinguishable to computers and for human visual inspections. The process of mutation detection is automated. The software processes up to 400 lanes of data in 1 minute providing a concise reporting of all mutations detected. Mutation Output Report Concise reporting of Mutation Discovery Findings: Up to 400 Lanes of Data in 1 Report Exclusive Scoring Provides confidence factor of Mutation findings User definable information is exportable to LIMs or other data bases Easy Navigation to Actual Electropherogram of lane analysis...just double click Homozygous Mutations: Reference Trace The notated peak in the mutation electropherogram indicates a homozygous mutation. The mutation occurred outside the coding region where thick yellow arrow represents Genbank sequence from 3 to 5. Sample Trace Heavy Yellow Indicates coding region Mutation Electropherogram All mutations indicated by sharp peaks Mutation Confidence Scoring 2

3 Heterozygous Mutation: Quality Score of Sequence Trace The cyan color peak indicates the mutation with a base change from G to GC. The labeled number on the mutation peak are the mutation peak parameters such as peak intensity, area (x1000), overlapping factor, dropping factor, signal/noise ratio, and score. The line in the center of y axis indicates presence of insertion or deletion if red in color. Patented algorithm utilizes 5 factors to determine presence of heterozygote mutations. Sensitivity is 1/10 of primary peak. Mutation Confidence Score Insertion & Deletions The central line shows an out-of-scale peak at bases respective to the Genbank file. The deletion mutation is indicated by a positive peak and insertion mutation shows the negative peak. Heavy red indicates position of indel; center line turns from green to red to alert you pr presence of insertion or deletion. Program handles up to 100 bp Indel Citation list: Rajagopalan H, Bardelli A, Lengauer C, Kinzler KW, Vogelstein B, Velculescu VE. Tumorigenesis: RAF/RAS oncogenes and mismatch-repair status. Nature 2002 Aug 29;418(6901):

4 Mutation Surveyor Variant Detection from Forward and Reverse Sequence traces Mutation Surveyor s exclusive capability of performing variant analysis on forward and reverse sequence pairs provides superior accuracy (>99%), high sensitivity (1/10th of primary peak) and ultra low false positive rate (<50 per million bases) when sequences of Phred 20 are used. Surveyor is an excellent choice for confirmational analysis and diagnostic applications. As with Mutation Explorer, Surveyor accepts sequence traces from all platforms and chemistry, slab gel or capillary electrophoresis. Additionally Surveyor has a myriad of special tools to assist in your analysis, such as the ability to simplify editing of Genbank.seq files; two ways to create synthetic reference files, special customized reporting functions and many others. Surveyor can be fully automated for unattended analysis, and is capable of performing analysis on 100 sequence pairs in approximately 2 minutes. Analysis Reporting Surveyor reports analysis results in 3 concise formats: by sample; by Forward & Reverse Sequence pairs, and in a global format. Variants are listed in base pair order, with allele frequency calculated and indicated at the bottom of the reports. Each samples is linked to set of electropherograms for rapid and easy confirmation. Mutation Report Lists all found variants in sample order. Paired Report, Variants in bp order, allele frequency indicated at bottom Global Report with Allele Frequency 4

5 Mutation Surveyor detects all DNA variants utilizing our exclusive anti correlation technology providing: Accuracy, greater than 99% High Sensitivity, to 1/10th of primary peak Low False Positives, less than 50 per million bp analyzed Mutation Surveyor and Explorer exclusive detection technology compare the physical sequence traces of reference and sample significantly enhancing the variant detection of programs utilizing base call text. SoftGenetics technology avoids the errors of text based Variant Detection Programs which are dependent upon the accuracy of the text base call. (Occurrence of DNA variants is approximately 1-1,000 bases, base call text, at Phred 20 has an accuracy of 99%, an order of magnitude of inaccuracy below the incident rate of DNA variants.) Mutation Surveyor detects Heterozygote, Homozygote, and up to 100 bp Indels: Heterozygote Mutation, patented technology is sensitive to 10% of primary peak. Homozygote Mutation, Electropherogram set is linked to report for quick confirmation. Deletion Insertion Mutation Surveyor provides quality reporting on sequence quality and color coded mutation confidence scoring. Found variants are shown as sharp peaks in the center two mutation electropherograms, easily identifiable by com- 5

6 Give Mutation Explorer & Surveyor a try: A fully functional no charge 30 day trial program, complete operation manual and quick user guide and other mutation discovery links can be downloaded at our website: All we ask is to let us know how Mutation Explorer assisted in your work. Students: We have developed a special 48 lane version of Mutation Explorer designed especially for students to increase accuracy and productivity. The student version is offered at an exceptional price, so we require proof of student status. Please contact us regarding full details. System Specifications: Operating System: Microsoft Windows 2000, NT,XP Processor: Pentium III or higher, 500 MHz RAM: 256 MB Hard Drive: 1GB available Mutation Explorer and Surveyor are designed for use on desk top PC s. Ordering Information Prices in US Dollars Product Num ber Description Industrial Users Academ ia/hospitals/ Governmental ME Mutation Explorer, Single User license US$ US$3, ME Additional User Licenses, cost each ME Additional 12 months U pgrades 1, , ME MS MS MS MS Student Version, Mutation Explorer, single user license n/a Mutation Surveyor, Single User license 7, , Additional User Licenses, cost each Additional 12 months U pgrades 2, , Student Version, Mutation Surveyor, single user license n/a Initial User License includes 12 m onths of upgrades from date of purchase SoftGenetics, Inc. 459 Park Lane State College, PA 16803, USA /

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