Publications & Literature

• SOLiD™ Software: Data Analysis and Management
• SOLiD™ System Barcoding

• Whole Genome Resequencing
• Whole Genome Sequencing of E. coli Bacteria
• Mate-Paired Libraries Detect/Define Genetic Rearrangements

• Microdroplet-based PC R enrichment of genomic regions for targeted sequencing on the SO LiD® System
• Array-based Enrichment of Specific Genomic Regions using the SOLiD™ System
• Targeted Resequencing and Rare Allele Detection
• SureSelect™ Solution-Based Enrichment of Genomic Regions for Targeted Resequencing on the SOLiD™ System

• Whole Genome Sequencing of E. coli Bacteria
• First complete genome sequence of infectious laryngotracheitis virus Publication: BMC Genomics (2011) Authors: Lee S. et al.

• SOLiD™ High Throughput Analysis of Differential Gene Expression

• miRNA Discovery and Profiling with the SOLiD™ Small RNA Expression Kit
• Whole Genome Analysis of Small RNA

• Analysis of Protein-DNA Interactions With the SOLiD™ ChIP-Seq Kit

• Effective Strategies for Exon/Exon Junction Mapping and Fusion Transcript Detection
• Whole Transcriptome Profiling Using the SOLiD™ 3 System
• Single-Cell Whole Transcriptome Profiling with the SOLiD™ System

• Fractionation of Differentially Methylated Regions with the MethylMinerâ„¢ Methylated DNA Enrichment Kit and Deep Sequencing with the SOLiD™ System

Application Fact Sheet

• SOLiD™ System Accuracy

Brochures

• Product Bulletin: SOLiD™ Total RNA-Seq Kit
• TarqetSeq™ Exome Custom Enrichment Kit Product Bulletin

Quarterly Newsletter

• The SOLiD Read August 2011
• The SOLiD Read February 2011

Specification Sheet

• 5500 Series Genetic Analyzer System Specification Sheet
• Library Builder Specification Sheet
• SOLiD™ EZ Bead™ System Specification Sheet
• LifeScope Genomic Analysis Solutions Specification Sheet

White Papers

• SOLiD™ System Accuracy with the Exact Call Chemistry Module
• 2-Base Color Codes and Its Application to Annotation, Error Detection, and Error Correction

• AGBT 2011 - Accurate detection of insertions and deletions
• AGBT 2011 - Getting personal: improved throughput and accuracy toward enhanced understanding of human genome biology
• AGBT 2011 - Towards a pushbutton human genome
• AGBT 2011 - Low input mate-paired sequencing and its application on FFPE tumor samples
• AGBT 2011 - Real-time data quality feedback for the 5500 Series SOLiD™ Sequencers
• AGBT 2011 - High accuracy base space sequencing: results from error-correction ligation chemistry
• AGBT 2011 - Accuracy and performance breakthroughs with the 5500 Series SOLiD™ Sequencers
• AGBT 2011 - Analysis of a Southern African genome using SOLiD™ System error correction codes
• Increased read length on the SOLiD™ Sequencing platform
• Multiplex sequencing on the SOLiD™ platform with 10, 16, or 96 barcodes
• SOLiD™ System Sequencing and 2 Base Encoding
• Accurate genome-wide SNP detection with low and medium coverage with next-generation sequencing
• Paired end sequencing on the SOLiD™ platform
• Enhanced Throughput and Accuracy on the SOLiD™ System.
• BioScope™ 1.2: An Applications Framework for SOLiD™ Sequence Data Analysis.
• Application specific accuracy with SOLiD™ System high throughput sequencing
• ESHG 2011 - Simultaneous Evaluation of Small RNA, Whole Transcriptome, Whole Genome, ChipSeq and Targeted Resequencing on Next Generation Sequencing Platforms
• ESHG 2011- P12.045 Detection of low frequency variation in heterogeneous samples using the accuracy and sensitivity of a SOLiDTM System

• ABRF 2011 - Robotic scripts, methods, reagents, and devices for high throughput automated production of next generation sequencing DNA fragment libraries
• AGBT 2011 - Methods and reagents for automating DNA fragment library construction on commonly available liquid handling robotic platforms
• AGBT 2011 - A New protocol for next gen library construction increases yield / complexity and simplifies parallel sample handling

• Lorne 2011 - Preliminary description of the genome of the single individual from northern Europe
• AGBT 2011 - Accessing the inaccessible genome
• Paired end sequencing of human genomes on the SOLiD™ platform
• Increased Read Length on the SOLiD™ Sequencing Platform.
• The Detectable Genome: How much of the human genome is accessible to variant discovery by next-generation sequencing?
• Large-Scale SNP Detection via Ligation-based Dibase Sequencing Across Multiple HapMap Individuals: NA18507, NA19240, and NA12878
• Accurate genome-wide SNP detection with low and medium coverage with next-generation sequencing
• Dibase sequencing allows accurate SNP detection at moderate and low coverage with diBayes algorithm
• Functional analysis of the genetic variation within the genomes of three HapMap individuals obtained by whole-genome, second-generation sequencing
• Sequence and Structural Variation in a Human Genome
• Resolving Structural Variations Using SOLiD™ Mate Pair Sequencing Technology
• A high-resolution structural variation map of human germline genomes by next-generation, high-throughput paired end sequencing with the SOLiD™ System
• Whole Genome Resequencing with Short Reads: Accurate Mutation Discovery with Mate Pairs and Quality Values
• Finding Indels with Short Sequencing Reads and De Novo Assembly with SOLiD™ Reads
• Genome Variablility Analysis of Yoruba in Ibadan, Nigeria (NA18507) by SOLiD™ Mediated Whole Genome Re-Sequencing
• Next-generation Sequencing for Detection of Rare Variants and Heterozygosity
• Single Base-pair Breakpoint Resolution Map of Small to Large Indels Using a Split Read Technique with High-throughput Mate-pair and Fragment Sequencing
• Whole-Genome SNP Detection and Haplotype Phasing with Mate Pairs via Ligation-Based Dibase Sequencing
• The normal and tumor spectrum of copy number variation: Copy number alterations correlate with changes in gene expression in tumor transcriptome.
• Genome-wide discovery of copy number variations in cancer patients using SOLiD™ sequencing

• AGBT 2011 - Multiplex exome enrichment from pooled barcoded libraries yields efficient SNP and indel detection on the SOLiD™ System
• PCR-based targeted sequence enrichment for next generation sequencing platform.
• DiBayes: A SNP Detection Algorithm for Next-Generation Dibase Sequencing
• Applications of Next Generation Sequencing in Genetic Epidemiology
• SNP discovery in high-throughput resequenced microarray-enriched human genomic loci.
• Multiplexed Target Enrichment for SOLiD™ System Sequencing
• Solution-Based Enrichment of Genomic Loci for Massively Parallel Sequencing on the SOLiD™ System
• MHC Haplotype Sequencing: An Integrated Approach to Common Disease
• Targeted sequence enrichment for the SOLiD™ System

• AGBT 2011 - Single molecule real-time DNA squencing using FRET-based reagents
• Increased Read Length on the SOLiD™ Sequencing Platform.
• Finding Indels with Short Sequencing Reads and De Novo Assembly with SOLiD Reads
• Genome completion by SOLiD™ System Next Generation Sequencing.
• Rapid, Short-Read Sequencing and Comparison of 8 Different Listeria Strains.

• Rapid chromatin oreparation from solid mammalian tissues for low cell ChIP assays
• SOLiD™ ChIP-Seq kit for ChIP & ChIP-sequencing from low number of cell & tissue samples
• SOLiD™ ChIP-Seq Kit for ChIP and ChIP-Seq with Low Cell Number Samples.

• AGBT 2011 - RNA-seq for identifying gene expression changes associated with relapse in acute lymphoblastic leukemia (ALL)
• Multiplex sequencing on the SOLiD™ platform with 10, 16, or 96 barcodes
• Gene Expression in human samples using SOLiD™ Next Generation Sequencing.
• ESAT 2011 - Comparative Analysis of CHO Cell Transcriptional Dynamics under Different Cell Culture Conditions using Next Generation RNA Sequencing Technology

• ABRF 2011 - MicroRNA analysis using RNA extracted from matched formalin-fixed paraffin-embedded (FFPE) and fresh frozen samples on SOLiD™ system
• AGBT 2011 - SOLiD™ System approaches for small RNA expression profiling of formalin-fixed, paraffin-embedded (FFPE) tissue samples
• An Expression Atlas of small RNAs generated using the SOLiD™ Sequencing System
• Multiplex Sequencing on the SOLiD™ Platform with 10, 16, or 96 Barcodes
• A novel approach for miRNA profiling using massively parallel, ligation-based sequencing
• Analysis of the Molecular Factors Controlling Human Osteosarcoma Response to Chemotherapy

• ABRF 2011 - Improvements in SOLiD™ whole transcriptome library preparation workflow to enable low input RNA amounts
• ABRF 2011 - Development of ERCC RNA spike-in control mixes
• ABRF 2011 - Use of synthetic transcript pools to evaluate RNA-Seq performance and analytical methods
• AGBT 2011 - RNA-Seq for identifying gene expression changes associated with relapse in Acute Lymphoblastic Leukemia (ALL)
• Identifying novel expressed gene fusions in MCF-7 cell line using next generation sequencing
• Multiplex sequencing on the SOLiD™ platform with 10, 16, or 96 barcodes
• Whole transcriptome analysis of total human RNAs by massively parallel sequencing on the SOLiD™ system
• SOLiD™ sequencing unravels transcriptome
• Single cell transcriptome analysis on the SOLiD™ system
• A comparison of next generation sequencing and microarrays for whole transcriptome expression profiling
• mRNA-Seq Whole Transcriptome Analysis of a Single Cell
• Whole transcriptome sequencing of three oral cancers
• Multiplex Single Cell RNA-Seq Transcriptome Analysis of Pluripotent Cells both in vitro and in vivo
• IADR 2011 - The Saliva RNA Interactome

• AGBT 2011 - Sequencing of methylated human DNA enriched through MBD-Affinity is a cost-effective alternative to whole genome bisulfite conversion
• Genome-wide methylation data analysis on the SOLiD™ System
• Efficient whole-genome DNA methylation analysis of the Human Reference Genome
• Sequencing of Methylated DNA Enriched with Methyl-CpG-binding domains.