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Genotyping project

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A light-directed chemical synthesis of oligonucleotide arrays was carried out by the company. Genomic DNA was amplified by multiplex PCR over a long distance, then all PCR products intended for one genotyping array were combined together and labeled with biotinylated nucleotides. Each labeled DNA sample was hybridized to the chip. The hybridized chips were washed, then incubated with streptavidin, washed and incubated with biotinylated anti-streptavidin antibody, followed by another wash. Then the chips were stained with streptavidin-cychrome conjugate, followed by washing. Sample-array hybridization was detected using a confocal laser scanner.

Individual genotypes for SNPs were determined by clustering measurements across multiple scans in a two-dimensional space defined by the corrected against the background intensity of the ideal match traits for the reference and alternative alleles.

Biochips

Represents  hybridization  a nucleic acid sample (target) with a very large set of oligonucleotide probes that are attached to a solid support for sequencing or detecting changes in the sequence or expression of a gene, or for mapping genes (grid).

Several competing technologies have emerged for the introduction of microchip probes. Biotech53  pioneered this field, using in situ synthesized oligonucleotides as probes and developing microarrays in silico, thereby eliminating the need to manage clone libraries.

Microchip technology has two main uses:  gene expression analysis  and analysis  genetic variations .

Background research

The DNA sequence of any two people is 99.9 percent identical. However, these differences can significantly affect a person's risk of illness. The regions in the DNA sequence where individuals differ in one DNA base are called single nucleotide polymorphisms ( SNPs ). Sets of neighboring SNPs on the same chromosome are inherited in blocks. This SNP template on the block is  haplotype . Blocks can contain a large number of SNPs, but several SNPs are sufficient to uniquely identify haplotypes in a block. A gapmap is a map of these blocks of haplotypes, and the specific SNPs that identify the haplotypes are called tag SNPS.

The Hap map should be valuable by reducing the number of SNPs required to study the entire genome for phenotype association, from the 10 million SNPs that exist to about 500,000 SNP tags. This will make approaches to scanning the genome to find regions with genes affecting diseases much more efficient and comprehensive, since efforts will not be wasted by typing more SNPs than necessary and all regions of the genome can be included.

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Biotech53 portable high performance nanopore sequencer, combining sequencing unit and control station with display, designed to run one standard R9 or R10 flow cell.

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Main advantages 

  • Belongs to the 3rd generation NGS sequencers;

  • Simple and fast sample preparation without amplification;

  • Long readings without length limit;

  • Maximum productivity up to 30 - 45 billion nucleotides;

  • Low cost per nucleotide read;

  • Ability to track parameters: control the sequencing process and carry out base-scaling in real time;

  • The device is very light (450 g) and compact (30 x 14 x 11.6 cm);

  • Mobility: the device does not require a special room to operate, it can be used in the "field" conditions and moved even during operation;

  • The control station and display are wired into the device case. Primary data processing can be performed in real time with the ability to upload sequences to an external medium;

  • The software runs on the resources of the GPU, which speeds up data processing by ~ 30 times;

  • The ability to stop the launch at any time.

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