ROH size Class | SNP Array | WGS low coverage | WES | Applications |
---|---|---|---|---|
Short < 1 Mb | Poor performance due to low SNP coverage. Can be adjusted to detect ROH by modifying the number of SNPs required in a ROH. | Able to detect but need to build adjustment for genotype calling errors. | Able to detect but only in selected genomic regions. Software like H3M2 allows meaningful regional analysis [39]. | Detection of rare variants involved in deleterious recessive alleles and directional dominance [11, 12]. Analysis of LD patterns and extreme bottle necks [33]. |
Medium 1-8Â Mb | Able to detect if the array has at least 300Â K SNPs. ROH boundaries will be fuzzier in comparison with WGS low coverage data. | Good performance but need to build adjustment for genotype calling errors. Allowing 3 heterozygous SNPs per ROH would grant meaningful outcomes. | Able to detect, but only in selected genomic regions and boundaries of ROH could be fuzzy if they reach into non-exonic regions [49]. | Detection of rare variants involved in diseases. Analysis of inbreeding depression. Genome architecture and ROH island detection [50]. Population history, bottle necks, remote consanguinity and genetic drift [51]. |
Long > 8 Mb | Good performance if the array has at least 300 K SNPs. | Good performance but need to build adjustment for genotype calling errors. Allowing 3 heterozygous SNPs per ROH would grant meaningful outcomes. | Poor performance due to short size of most exons and their sparsity across the genome. | Analysis of inbreeding depression. Validation of GWAS findings. Population history and cultural practices, close consanguinity [6, 41]. |