Shared Genomic Segment (SGS) analysis is a gene mapping strategy for use in single extended high-risk pedigrees. SGS identifies regions of interest that segregate to multiple cases in a large pedigree. The identification of such regions is helpful for interrogating sequencing data, especially when functionally-relevant disease-involved variants are complex (e.g. non-coding, copy number variation) and not easily identified in a direct-to-sequencing/functional-annotation strategy. SGS has optimal power in pedigrees containing multiple cases with at least 15 meiotic events separating the cases. SGS first identifies all genomic segments shared identical-by-state (IBS, sharing without regard to inheritance) in the cases. IBS segments are then assessed for being significantly longer than expected by chance. If significantly longer at a genomewide significance level, then inherited sharing due to the shared disease is implied –chance sharing in distant relatives is extremely improbable. The tool uses high-density genome-wide SNP data (single nucleotide polymorphisms), which can either be directly from a genotyping platform or extracted from sequence data.

• Manuscript
• Code
• Documentation
• Dr Alun Thomas's JPSGCS (as used by SGS) is available here