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Enhanced INDEL Detection from Sanger Sequence Traces

Mutation Surveyor software employs a rigorous alignment algorithm to detect both deletions and duplications from Sanger Sequencing reads. Compatible with the outputs from all major DNA capillary electrophoresis platforms, including Applied BioSystems Prism, MegaBACE as well as Beckman Coulter CEQ platforms, Mutation Surveyor’s unique technology accurately detects homozygote and heterozygote insertions and deletions, and automatically de-convoluting het-indels, providing accuracy, sensitivity and ease-of-use not found in similar DNA sequence analysis programs such as DNAStar, Sequencher, Variant Reporter or SeqPilot.

Mutation Surveyor software utilizes a robust multi-step alignment algorithm which is capable of aligning sequence traces containing up to 20% variation from the reference. The first step of the alignment process utilizes 12bp seed to align the sample to reference, if a gap occurs the algorithm reduces the seed size to 3bp in the local region, followed by the Smith-Waterman algorithm to complete local regional alignment. As the alignment occurs the software automatically gaps either the reference (insertion/duplication) or gaps the sample (deletion). The central line of the Mutation Electropherogram turns from green to red indicating the INDEL detection, placing a heavy red line above the INDEL location.

Mutation Surveyor robustly detects INDELS, even in the presence of up 20% variation
from the reference sequence.

Insertions and deletions are found by monitoring the mobility of the sample DNA fragments, again in comparison to the reference, providing an extremely low false positive rate and ignoring the miscalls or overcalls from basecaller software. In the event that a heterozygote insertion or deletion is detected, the software will de-convolute the multiple patient trace into two clean traces, while continuing with the mutation detection.

76 bp Insertion

Heterozygote Insertion / Deletion

The position of the Indel is indicated by the heavy red line.

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Mutation Surveyor Capabilities:
Detection Sensitivity & Accuracy
INDEL Detection
INDEL de-Convolution
Somatic Mutation Detection
Mutation Quantification
Methylation Analysis
Hypervariable Region Variant Detection
Reference Assembly
Custom Reporting Options
Alignment of Reads
Mitochondria DNA Sequence Analysis
Base Calling
Unattended Operation 

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