Pediatric Genomic Medicine Software Tools
Pediatric Genomic Medicine Software Tools

The Center for Pediatric Genomic Medicine uses the latest software programs to conduct genome sequencing and other research projects.

Rapid Understanding of Nucleotide variant Effect Software (RUNES)

RUNES is a multi-stage analysis pipeline for annotating and classifying human nucleotide variation detected through short read alignment. The long-term plan is to continually add characterizations and variant types as new tools/capabilities appear.
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ACMG classification

Variant classification is the final stage of variant characterization and consists assigning an interpretive category representing clinical significance to each variant. The ACMG categories rely heavily on the identification of novel vs. known variants which implies comparison to external variation databases.
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Symptom and Sign Assisted Genome Analysis

Matching of clinical features to diseases to disease genes is performed by entry of terms describing the patients presentations into a novel clinico-pathologic correlation tool (SSAGA, Symptom and Sign Assisted Genome Analysis).
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Minor Allele Frequency

The Variant Warehouse records a Minor Allele Frequency for all variants observed through CPGM sequencing projects. This frequency value simply records the number of samples that have each variant in them along with the total number of samples sequenced to date. These values are recalculated for every variant in the Variant Warehouse after the completion of each RUNES run so that the value properly records the presence of absence of each variant across every sample represented in the database. 

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