NGS SEQUENCING NEW TECHNOLOGY
HiSeq sequencer is an advanced sequencing method that uses Illumina technology. This enables to receive up to 600 GB (600x nucleotides) in 6 trillion paired end reads during 11 days. It consists of 16 lines on which sequencing is performed separately. For each line, 170 million of PE reads is generated.
MiSeq sequencer employs sequencing-by-synthesis Illumina technology, which allows to obtain up to 15 GB (15×109 bases) in 45 million paired reads from one sequencing trial. MiSeq is the only desktop sequencer that can produce 2 x 300 paired-end reads in a single run. This allows small genome sequencing and assembly, and enables detection of target variants with unmatched accuracy, especially within homopolymer regions. Now, even more samples can be processed in less time while generating more reads per run than any previous versions. All of this can be achieved using the targeted gene and small genome sequencer with the shortest sample-to-data workflow.
CURRENTLY AVIABLE APPLICATIONS:
– amplicon sequencing,
– genetic predisposition panels:
· Cancer panels o germline mutations (genetic predispositions) – entire spectrum or specific cancer panels:
· Panel 170 PLUS includes genes associated with both common (e.g., breast cancer, prostate, hematologic malignancies, colorectal, lung, kidney) and rare cancers. Targets over 1700 exons, spanning 94 genes of interests and additional 284 SNPs occurring in 78 different genes associated with predisposition towards cancer.
· Panel “For Him” includes genes associated with the most common male cancers, like: prostate cancer, colorectal cancer, lung cancer, testicular germ cell tumor. Targets exons spanning 54 genes of interests and additional 45 SNPs in 45 different genes associated with predisposition towards the most common male cancers.
· Panel “For Her” includes genes associated with the most common female cancers, like: breast, colorectal, lung and ovarian cancer. Panel “For Her” targets exons spanning 48 genes of interests and additional 22 SNPs in 22 different genes associated with predisposition towards the most common female cancers.
· Cardiomyopathy panel – targets 46 genes linked to inherited cardiomyopathy. This Panel targets genes linked to inherited cardiomyopathies, including Hypertrophic Cardiomyopathy (HCM), Dilated Cardiomyopathy (DCM), Restrictive Cardiomyopathy (RCM), Arrhythmogenic Right Ventricular Cardiomyopathy (ARVC), Catecholaminergic Polymorphic Ventricular Tachycardia (CPVT), and Left Ventricular Non-Compaction (LVNC). Additional content covers several syndromes, including Danon and Fabry disease, Barth syndrome, and Transthyretin Amyloidosis — all of which can be present with isolated cardiomyopathy.
· Autism panel – targets over 1 700 exons, spanning 101 genes linked specifically to autism. These are genes reported in the Online Mendelian Inheritance in Man (OMIM) database for autism research; genes with recurrent mutations resulting in developmental disability; genes with reported mutations found in case of studies involving developmental disability characteristics; and combined autism-relevant genes (e.g., AutismKB). Genes neighboring strong association signals were excluded in the absence of published reports of mutations.
Price-list for MiSeq experiments:
De novo sequencing is crucial for better understanding of organisms functioning. It allows us to explore the whole genome without the need to use any reference sequences. De novo genome sequencing can be carried out for each organism, a plasmid, an artificial chromosome, etc.
Whole genome and amplicons resequencing
Exome sequencing (targeted exome capture) is an efficient strategy to selectively sequence coding regions of the genome as cheaper and still effective alternative to whole genome sequencing. Exome sequencing involves sequencing of protein coding regions and around 200 surrounding nucleotides. Exome sequencing is particularly important in the analysis of rare mutations associated with genetic disorders that can be reliably interpreted using a variety of publicly available genetic databases (e.g. dbSNP).
Metagenomics: Sequencing of hipervariable regions of 16S RNA gene
16S ribosomal RNA (rRNA) sequencing is a common amplicon sequencing method used to identify and compare bacteria present within a given sample. 16S rRNA gene sequencing is a well-established method for studying phylogeny and taxonomy of samples from complex microbiomes or environments that are difficult or impossible to study. Data from 16S studies are used to improve the sensitivity and specificity of taxonomic assignments, down to the species level.
Unlike capillary sequencing or PCR-based approaches, next-generation sequencing (NGS) is culture-free method that enables analysis of the entire microbial community within a sample, including identification of species that may not be found using other methods. With the ability to combine many samples in a sequencing run, microbiology researchers can use NGS-based 16S rRNA sequencing as a cost-effective technique to identify strains that may not be found using other methods.
Thanks to its speed, efficiency and accuracy, NGS sequencers offer a new option for the classic RNA sequencing and transcriptome analysis. Transcriptome is the full set of transcripts, comprising mainly mRNA, but also small RNA molecules such as tRNA and rRNA. RNA-seq method is an alternative for expression microarray. Analysis can be performed for every species for which there is a reference genome. Furthermore, expression data received from the NGS sequencer can be analyzed using many of the tools commonly used in the microarray analysis, in the hierarchical clustering.
ChIP-Seq is a powerful tool for genome-wide mapping of histone modifications, protein-DNA interactions, and identifying consensus protein-binding sites in DNA. By combining chromatin immunoprecipitation (ChIP) and massively parallel sequencing, ChIP-Seq can be used to accurately survey interactions between protein, DNA, and RNA, enabling the interpretation of regulation events central to many biological processes and disease states.
Leveraging Illumina’s industry-leading sequencing technology, ChIP-Seq can identify a broad range of protein/nucleic acid interactions with confidence, generating millions of counts across multiple, indexed samples per lane for cost-effective and precise analysis.