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Table 1 Summary of throughput, length, quality, and cost of current versions of genomic sequencing.

From: Genomic sequencing in clinical trials

Platform

Throughput

Length

Quality

Cost

Applications

Sources of error

Advantages

Disadvantages

Sanger

6 Mb/day

1,000 nt

10-4-10-5

~$500/Mb

Small sample sizes, genomes, SNPs, long haplotypes, low complexity regions, etc.

Polymerase/amplification, low intensities/missing termination variants, contaminant sequences

Longest reads, gold standard for validations

High cost, low throughput

454/Roche

750 Mb/day

400 nt

10-3-10-4

~$20/Mb

Complex genomes, SNPs, structural variation, indexed samples, small RNAs, mRNAs, etc.

Amplification, mixed beads, intensity thresholding, homopolymers, phasing, neighbor interference

Longer reads, easier to assemble

Medium throughput, expensive, indel errors more likely

Illumina

5,000 Mb/day

100 nt

10-2-10-3

~$0.50/Mb

Complex genomes, counting (SAGE, CNV Chip, small RNA), mRNAs, structural variation, bisulfite data, indexing SNPs, etc.

Amplification, mixed clusters/neighbor interference, phasing, base labeling

Lower cost, widely adopted platform, most well-developed bioinformatics efforts

Higher base substitution error rate, shorter reads

SOLiD

5,000 Mb/day

75 nt

10-2-10-3

~$0.50/Mb

Complex small genomes, counting (SAGE, ChiP, small RNA, CNV), SNPs, mRNAs, structural variation, indexing, etc.

Amplification, mixed beads, phasing, signal decline, neighbor interference

Lower cost, 2-base encoding chemistry, higher per-base accuracy

Shortest read lengths,

still an emerging platform

  1. Adapted from Kircher, et al. Bioessays 201010