Journal: Current allergy and asthma reports

Article Title: Novel Sequencing-based Strategies for High-Throughput Discovery of Genetic Mutations Underlying Inherited Antibody Deficiency Disorders

doi: 10.1007/s11882-011-0211-x

Figure Lengend Snippet: Performance comparison of common sequencing detection platforms

Article Snippet: Currently, the enriched target sequences are detected by three approaches: traditional Sanger sequencing, NGS, and high-density oligonucleotide microarray ( ). table ft1 table-wrap mode="anchored" t5 caption a7 Sanger sequencing Resequencing microarray Next-generation sequencing Latest platform ABI 3730xl DNA Analyzer a Affymetrix Custom Resequencing Array b Roche 454 GS FLX Titanium Illumina Solexa GA II SOLiD 4 Sequencing chemistry Dideoxynucleotide chain termination Sequencing by hybridization Pyrosequencing Reversible terminator sequencing by synthesis Sequencing by dinucleotide ligation Preferred template DNA Cloned or PCR-amplified DNA Mixture of PCR-amplified targets Mixture of DNA fragments captured by hybridization and amplified by universal primers Run time 2 h 16 h for hybridization 10 h 2–4 d 6–8 d Read length 500–1,100 bases Not limited Up to 500 bases 35–75 bases 25–75 bases Data output 96 kb/run 300 kb/array 400 Mb/run 3–8 Gb/run 10–20 Gb/run Estimated cost c ~$1–$2 per read $300/array $60/Mb $2/Mb $2/Mb Preferred mutations SNP and indel SNP SNP and indel SNP SNP Raw base call accuracy, % >99.99 Up to 99.99 for haploid genomes ~99.5 >99 ~99.95 Limitation 1 target per reaction Only unique known sequence or known indels targeted Homopolymer detection problems Short sequence reads, indel detection and homologous sequence alignment problems; need strong central processing unit power and bioinformatics support Sequencing applications Low-throughput, mutation confirmation Mid-throughput resequencing High-throughput, de novo sequencing High-throughput resequencing High-throughput, highly accurate resequencing Open in a separate window a Life Technologies Corp., Carlsbad, CA b Santa Clara, CA c Does not include cost of target sequence enrichment and capital equipment for sequencing Mb megabyte; PCR polymerase chain reaction; SNP single nucleotide polymorphism ( Data from Kothiyal et al. [ 36 ], Metzker [ 37•• ], Nowrousian [ 48 ], Voelkerding et al. [ 52 ], Hacia [ 53 ], and Voelkerding et al. [ 62 ].)

Techniques: Sequencing, Microarray, Next-Generation Sequencing, Hybridization, Ligation, Clone Assay, Amplification, DNA Sequencing, Mutagenesis