SNPtrio

SNPtrio analyzes SNP microarray data from mother–father–child trios to identify regions of uniparental inheritance (UPI), Mendelian inconsistency (MI), uniparental disomy (UPD), deletions, and related inheritance patterns for genetic interpretation.

Key Features:

• Trio-based SNP analysis: Analyzes genotype patterns specifically in mother–father–child trios to assess inheritance.
• UPI and MI detection: Locates regions exhibiting uniparental inheritance (UPI) and Mendelian inconsistency (MI) within SNP data.
• Parental origin assignment: Distinguishes paternal versus maternal origin of alleles in identified regions.
• Iso- versus heterodisomy classification: Differentiates iso-disomy and hetero-disomy to classify types of UPD.
• UPD detection: Identifies uniparental disomy events from SNP genotype patterns.
• Deletion detection: Identifies hemizygous and homozygous deletions and microdeletions from SNP data.
• Statistical assessment: Computes probability values assessing whether observed inheritance patterns could occur by chance.
• Nonparental relationship detection: Identifies nonparental relationships such as nonpaternity/nonmaternity.
• Parent-of-origin in aneuploidy: Determines the parental origin of extra chromosomal copies, e.g., in trisomy 21.
• Platform validation: Validated on Affymetrix 10K and 100K arrays and Illumina 550K arrays and on samples with FISH-confirmed microdeletions.
• Visualization of inheritance patterns: Provides visualization and analysis of inheritance pattern distributions across the genome.

Scientific Applications:

• UPD identification and classification: Detection and classification of uniparental disomy events, including iso- and heterodisomy.
• Deletion and microdeletion detection: Identification of hemizygous and homozygous deletions and validation against FISH-confirmed cases.
• Parent-of-origin determination in aneuploidy: Assignment of parental origin for extra chromosomes in trisomy 21 analyses.
• Diagnosis-related analyses: Applied to cases involving Prader–Willi syndrome, Angelman syndrome, Beckwith–Wiedemann syndrome, pseudohypoparathyroidism, and complex chromosome 2 abnormalities.
• Trio-based relationship assessment: Detection of nonparental relationships and assessment of transmission anomalies.
• Statistical evaluation of inheritance events: Quantitative assessment of the likelihood that observed inheritance patterns arise by chance.

Methodology:

Identifies regions of UPI and MI, distinguishes maternal versus paternal origin and iso- versus heterodisomy, detects hemizygous/homozygous deletions and UPD, and computes statistical probabilities for observed events.