Sequencing DNA gives us the ability to massively digitize the genetic codes and discover SNPs and other forms of mutations in the genome. This can increase our understanding, diagnosis, treatment and prevention of disease.
Comparative resequencing – (analyzing variations across and within species or samples subjected to different treatments) enables genome-wide association studies and provides a more comprehensive understanding that can enable development of personalized medicines and clinical diagnostic.
De novo sequencing has applications for medical, pharmaceutical, forensics, identification, defense, and basic research.
Transcriptome sequencing – gene expression profiling, exon sequencing, trans-splicing RNA sequencing, identification of novel transcripts, splice variant detection, transcriptional mutation, miRNA, small RNA, non-coding RNA, etc.
Sequencing only a part of the original sample by enriching – or depleting certain types of sequences. Target specific sequencing allows mainly the sequence(s) of interest to be determined.
Target-specific selection from a sample for a defined region by length or sequence, such as cancer suspect regions or known cancer genes, SNP regions, specific regions of interest (of unknown sequence).
Target-specific selection of RNA sequences, such as sets of coding genes known from databases, such as RefSeq mRNA or Ensembl gene, previous experiments, specific disease or pathway related RNAs, novel sets of RNAs, miRNAs, and biomarker RNAs.
General use of the capture probes on microarray to enrich target sequences.
Depletion of non-targeted sequences, such as depletion of those interfere with sequencing reactions, high abundance repeating sequences.
Reduction of the complexity in samples to enable multiplexing, high coverage, and high dynamic range or in-depth sequencing.
Obtain cleaner sequencing results to simplify data analysis and reduce time to final results.
Overcome the limitations of multiplex and/or long-range PCR. Take advantage of huge time and cost savings.
Sequence selection can be achieved by hybridization using complementary capture probes or by sequence-specific ligand molecules such as DNA/RNA binding molecules including small ligands, drug molecules, proteins/antibodies/peptides, aptamers, etc which bind to the sequence of interest.
In-Solution Target Selection
Capture probes can be used for solution hybridization. One method involves using oligonucleotides (OligoMix®) in solution as capture probes which are designed to target specific genomic/sequence regions of interest. After hybridization with a sample, magnetic beads are added and the capture probes are affinity linked to the beads. The captured target sequences are separated from other sequences by washing the beads after which the target sequences can be recovered. Another method involves using oligonucleotides (OligoMix®) immobilized on beads.
In target-specific selection for sequencing, often the goal is target sequence enrichment. Frequently it is more important to capture the highest possible percentage of the sequences of interest while sacrificing non-specific capture. In comparison, microarray hybridization requires high specificity for hybridization probes in order to obtain accurate signal reading for the genes analyzed. Through capture probe design, the degree of specificity can be varied according to experimental requirements. Capture probes can be designed to be as specific as microarray probes when this is required.
LC Sciences can synthesize custom oligonucleotides to serve as capture probes in your targeted sequencing application. Our OligoMix® product is a mixture of thousands of customer specified sequences delivered in a single tube.