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Candidate gene
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Any disease
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Easy to perform for one or two genes; requires no mapping, can directly identify the causative variant/mutation
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Relies heavily on current biological knowledge; success rate very low
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Genetic mapping by karyotyping
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Any disease
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Easy to perform; no familial cases required; can detect (large) balanced events
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Low resolution, only detects large chromosomal aberrations; mutation detection requires second step
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Genetic mapping by linkage analysis
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Inherited disease
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Easy to perform
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Requires large families, often identifies large loci; mutation detection requires second step
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Genetic mapping by homozygosity mapping
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Recessive monogenic diseases
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Small families can be used
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Most useful for consanguineous families; often identifies large loci; mutation detection requires second step
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Genetic mapping by CNV analysis
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Monogenic/monolocus disease
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High resolution CNV screening; no familial cases required; can potentially identify small loci
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Only investigates CNVs; cannot detect balanced events, no base-pair resolution; mutation detection requires second step
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Whole exome sequencing (WES)
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Any disease
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Base-pair resolution exome-wide; detects most types of genomic variation; can directly identify the causative variant/mutation
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Unable to detect non-coding variants; limited resolution for CNVs and other structural variation; coverage variability due to enrichment process; relatively expensive
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Whole genome sequencing (WGS)
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Any disease
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Base-pair resolution genome-wide; detects all types of genomic variation; can directly identify the causative variant/mutation
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Data analysis complex; even more expensive than exome sequencing
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