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Table 2 A comparison of next-generation sequencing methodologies

From: Genetic architecture of retinal and macular degenerative diseases: the promise and challenges of next-generation sequencing

Method

Advantages

Limitations

Applications

Whole-exome sequencing or candidate exome capture

Customized, economical compared to WGS, manageable data size

Captures genetic variants only in the coding regions of the genome; inefficient hybridization step; high DNA input; susceptible to capture bias

SNP and indel discovery in coding exons; suitable for the identification of causal genes in high-penetrance Mendelian diseases

Targeted re-sequencing

Customized, economical compared to WGS

Genetic variant discovery is limited by array design; high DNA input; inefficient hybridization step; captures only a small proportion of the genome

SNP and indel discovery; suitable for sequencing linkage intervals and genomic regions at or around associated signals

Whole-genome sequencing

Uncovers genome-wide coding and non-coding variants, no capture bias

Expensive; very large dataset; analysis methods are still evolving

Genome-wide SNP, indel and CNV discovery; suitable for rare variant discovery in Mendelian, complex or sporadic traits

Exome-chip

Cost-effective method for evaluating known rare variants (MAF of 1 to 5%)

Does not identify novel variants; limited to coding region; limited representation of intronic and regulatory variants

Genome-wide association analysis with rare variants

RNA-Seq

Array-independent profiling of the transcriptome

High coverage required for the identification of low-copy transcripts; not applicable for the identification of variants that cause loss of protein; limited by tissue- or cell-type availability

Genome-wide expression profiling; alternative transcript identification; non-coding RNA detection; SNP profiling; eQTL analysis

ChIP-Seq

Genome-wide profiling of epigenetic marks (DNA methylation and histone modifications) and cis-regulatory elements

Dependent on the quality of antibody; requires high input; analysis methods still evolving; high coverage needed for accurate profiling

DNA methylation; histone modifications; tissue-specific enhancer profiling