GTseq-Pipeline

GTseq-Pipeline enables genotyping of degraded, non-invasive samples using a highly multiplexed Genotyping-in-thousands by sequencing (GT-seq) approach to support genomics-based population monitoring.

Key Features:

• Highly multiplexed sequencing: Uses the Genotyping-in-thousands by sequencing (GT-seq) approach for targeted, multiplexed SNP genotyping.
• Targeted 324-SNP panel: Employs a specifically developed and validated panel of 324 single nucleotide polymorphisms optimized for polar bear genotyping from non-invasive samples.
• Degraded DNA compatibility: Capable of genotyping degraded DNA typical of non-invasive collections such as polar bear scat.
• Empirical genotyping success: Demonstrated successful genotyping for 85.7% of fecal samples confirmed to contain polar bear DNA.
• Contamination awareness: Addresses challenges posed by Next Generation Sequencing (NGS) contamination from non-target species when analyzing non-invasively collected samples.
• Cost efficiency: Provides a reduced cost per sample for targeted SNP genotyping compared to broader genomic approaches.

Scientific Applications:

• Individual identification: Differentiates individual polar bears using the targeted SNP panel.
• Sex determination: Enables sex assignment from non-invasive samples via genotyped markers.
• Relatedness assessment: Assesses relatedness among individuals using SNP-based genotypes.
• Population structure analysis: Resolves population structure within Canadian polar bear subpopulations using the targeted SNP data.
• Non-invasive population monitoring: Supports genomics-based monitoring from fecal and other non-invasive samples for conservation and management applications.

Methodology:

Applies highly multiplexed Genotyping-in-thousands by sequencing (GT-seq) using a validated 324-SNP targeted panel to genotype degraded DNA from non-invasive samples.