摘要:
A method for detecting hydroxymethylation modification in nucleic acid comprises: glycosylating the nucleic acid, digesting with MspI, ligating the digested fragments to a biotin-labeled linker at both ends thereof, digesting with NlaIII; capturing the digested fragments using streptavidin magnetic beads to produce fragments having the biotin-labeled linker at one end and a CATG 4-base sticky end at the other end, wherein these fragments reveal modification information of their adjacent CCGG sites; ligating the CATG sticky end to a linker containing a recognition site of MmeI or Ecop15I, digesting with corresponding restriction endonuclease to produce short sequence fragments that can reveal modification information of their adjacent CCGG sites; and performing a tag number comparison to obtain information about methylation and hydroxymethylation modification relative levels. A use of the method is also provided.
摘要:
Provided is a method of detecting method of detecting fusion transcripts in a sample to be analyzed. The method may comprises: subjecting the sample to be analyzed containing a RNA transcriptome to paired-end sequencing, to obtain paired-end RNA-Seq data of the sample to be analyzed; aligning the paired-end RNA-Seq data to a human reference genome sequence, to obtain first paired-end mapped reads, first single-end mapped reads, and first unmapped reads; evaluating an insertsize between two ends of the paired-end mapped reads by means of the first paired-end mapped reads, to obtain a proportion of paired-end mapped reads with overlapped 3′-ends; aligning the first unmapped reads to annotated transcripts, to obtain second single-end mapped reads and second unmapped reads; aligning the second unmapped reads to the annotated transcripts, to filter out unmapped reads caused by indel and obtain third unmapped reads; merging all single-end mapped reads, to obtain a set of single-end mapped reads; obtaining a gene pair linked by a cross-read as a primary set of candidate gene pairs based on the set of single-end mapped reads and combining with a relationship of the mapped paired-end reads; subjecting the primary set of candidate gene pairs to a filtration, to obtain a candidate set of fused gene pairs; bisecting the third unmapped read, to obtain a half-unmapped read; aligning the half-unmapped read to a gene-junction sequence in the candidate set of fused gene pairs, to obtain a potent region of a fused junction site in the gene in which the half-unmap read locates; outputting original reads of mapped half-unmapped reads, to obtain useful unmapped reads; subjecting the candidate set of fused gene pairs to a fusion simulation; aligning the useful unmapped reads to a junction library, to obtain a fused gene supported by the useful unmapped reads; calculating and gathering the fused sequence supported by the useful unmapped reads, to obtain information of the fused gene. And a system for detecting fusion transcripts is also provided.
摘要:
The present invention provides a method for constructing a high-throughput sequencing library, which comprises: fragmenting genomic DNA; end-repairing the DNA fragments; adding a base A to the 3′ end of the end-repaired DNA fragments; connecting the DNA fragments having cohesive end A with a methylated adapter; carrying out hybrid capture on the connection products by using specific probes to obtain object fragments; treating the object fragments with bisulfite, to convert non-methylated cytosines to uracils; PCR amplifying the converted object fragments; and separating and purifying the amplification products, wherein the amplification products constitute the high-throughput sequencing library. The present invention also provides a method and an apparatus for identifying methylation information in specified genome regions of a sample.
摘要:
Provided are a whole genome sample amplification method, a whole genome sequencing method, and a method for determining whether an abnormal state occurs in a whole genome, a whole genome sample amplification apparatus, a whole genome sequencing device, and a system for determining whether an abnormal state occurs in a whole genome. The whole genome sample amplification method comprises: subjecting a whole genome sample to a first amplification reaction, so as to obtain a first amplification product; and subjecting the first amplification product to a second amplification reaction, so as to obtain a second amplification product. The first amplification reaction is one of the PCR-based amplification reaction and the isothermal amplification reaction, and the second amplification reaction is the other of the PCR-based amplification reaction and the isothermal amplification reaction.
摘要:
The present invention relates to a method for optimizing the assembled result of sequencing data using a genetic map. In particular, provided in the present invention is a new method for assembling individual sequenced segments, which comprises the step of constructing the genetic map with a genetic marker. Furthermore, also provided in the present invention is a method for assembling the individual sequenced segments into a genome sequence, such as a chromosome sequence.
摘要:
The present invention relates to a method for quantifying the relative content of a protein in a sample. The present invention also relates to a method for comprising the relative content of a protein in at least two samples.
摘要:
Provided are the method and device for genetic map construction and the method and device for haplotype determination of a single cell. Wherein the method for genetic map construction includes: whole genome sequencing for at least a single cell from a same species, aligning the sequencing data to reference sequences respectively to determine genotypes of SNP sites, determining male parent a/female parent b typing results of SNP genotypes of a single cell based on the genotypes of SNP sites, dividing the chromosome of the species into linkage regions based on the male parent a/female parent b typing results of SNP genotypes, determining the variation ratio of a/b between two linkage regions to obtain recombination rate between every two continuous linkage regions, determining recombination map of a single cell according to the recombination rate, wherein the boundary site of a and b is the recombination site, determining the recombination rate of each recombination rate based on the recombination map to construct a genetic map of the species.
摘要:
The present invention provides an error correcting method of test sequence, which involves receiving test sequences, configuring high frequency short string list based on a preset high frequency threshold value, traversing each received test sequence, searching an area with the largest number of continuous high frequency short strings on each test sequence in combination with high frequency short string list, configuring whole left sequence and/or right sequence of high frequency short strings at left side and/or right side of searched area according to corresponding received test sequence and high frequency short string list, and constituting corresponding test sequence according to configured left and/or right sequence and searched area. The present invention also provides corresponding error correcting system of test sequence and gene assembly equipment.
摘要:
A method and an apparatus for genome assembly are provided. The method comprises: filtering a short-fragment-sequence output from end sequencing of an large insert-size library to remove unqualified sequence; aligning the filtered short-fragment-sequence onto a reference genome sequence, wherein, the filtered short-fragment-sequences comprise paired short-fragment-sequences; sorting the paired short-fragment-sequence after alignment into soap reads sequence, single reads sequence and unmap reads sequence based on the aligning result, and counting the number of each sort of sequence; calculating a distance between the paired soap reads on a fragment of the reference genome sequence, wherein a pair of the paired soap reads can be aligned onto a same fragment of the reference genome sequence; and counting a distance distribution of each pair of soap reads on the reference genome sequence; and assembling the genome sequence by using the paired single reads upon the distance distribution meeting a requirement of a threshold, wherein a pair of the paired single reads can be aligned onto two different fragments of the reference genome sequence.
摘要:
The present invention relates to methods, kits, and compositions for detecting and/or diagnosing metastatic potential of cancer cells or for evaluating prognosis in a patient with cancer by detection of the protein expression level of an HLA class I molecule and/or the copy number variation of a polynucleotide encoding the HLA class I molecule. The present invention also relates to the use of the protein expression level of an HLA class I molecule and/or the copy number variation of a polynucleotide encoding the HLA class I molecule as a prognosis biomarker and metastasis predictive biomarker of cancer.