Sequential sequencing

Inactive Publication Date: 2014-09-18
NUGEN TECH
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

[0011]In some embodiments, the directional nucleic acid library comprises closely related nucleic acid sequences as inserts. In some embodiments, the conserved regions within the nucleic acid inserts are located adjacent to variable regions. In some em

Problems solved by technology

Short read next generation sequencing (NGS) analysis has some limitations in both research and diagnostics.
One key drawback is the problem of phasing.
That is, when interrogating multiple loci of sequence variation, it is often impossible to determine which loci are co-located on the same chromosome or on the same chromosomal fragment.
On the other hand, if one of the inactivating mutations is present in the maternal chromosome and the other in the paternal chromosome, there is no functional copy of the gene product, resulting in a negative phenotype (non-viability, increased risk for disease and others).
Using short read sequencing, a muta

Method used

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Examples

Experimental program
Comparison scheme
Effect test

example 1

ization of the Human Oral Microbiome by Sequential Sequencing of Bacterial 16S Ribosomal DNA

[0045]This example describes the characterization of the human oral microbiome by sequencing of the 16S rRNA gene sequences of a number of related bacterial organisms. 16S rRNA gene sequences contain species-specific hypervariable regions that can provide means for bacterial identification.

Sample nucleic acid

[0046]Microbial genomic DNA is isolated from human saliva using the OMNIgene-DISCOVER sample collection kit (DNA Genotek) according to the manufacturer's instructions. Extracted DNA is then fragmented via sonication to an average length of 400 by and purified using Agencourt AMPure XP beads (Beckman Coulter Genomics).

Generation of control and test 16 S libraries with ligated adapters

[0047]The NuGEN Ovation Ultralow Library System (NuGEN Technologies) is used to generate two directional next generation sequencing libraries from 100 ng of the purified sample according to manufacturer's inst...

example 2

NA Sequencing—Distinguishing Between the SMN1 Gene and SMN2 Pseudogene Using Sequential Sequencing

[0050]Genomic DNA sequencing libraries are made using the NuGEN's Encore system. These libraries are sequenced on a DNA sequencing system such as those made by Illumina, Ion Torrent, Pacific Biosciences, or Complete Genomics. Following a first sequencing read, the DNA is denatured to wash away the first strand. A pool of primers that hybridize to common sequences in gene / pseudogene pairs are injected into the sequencer to act as a priming site for a second sequencing read. A primer set may include primers that will sequence through one of the nucleotide differences between SMN1 and SMN2 as well as primers that will generate sequence to read nucleotide differences, and therefore determine whether a sequencing read is from a globin gene or pseudogene. A combination of such primers will allow multiple gene / pseudogene pairs across the genome to be analyzed simultaneously for genetic mutatio...

example 3

DNA Sequencing Library

[0051]A targeted DNA sequencing library is made using the a target enrichment product from NuGEN, Agilent, Illumina, or Nimblegen. These libraries are sequenced on a DNA sequencing system such as those made by Illumina, Ion Torrent, Pacific Biosciences, or Complete Genomics. Following a first sequencing read, the DNA is denatured to wash away the first strand. A pool of primers that hybridize to common sequences in gene / pseudogene pairs are injected into the sequencer to act as a priming site for a second sequencing read. A primer set may include primers that will sequence through one of the nucleotide differences between SMN1 and SMN2 as well as primers that will generate sequence to read nucleotide differences, and therefore determine whether a sequencing read is from a globin gene or pseudogene. A combination of such primers will allow multiple gene / pseudogene pairs across the genome to be analyzed simultaneously for genetic mutations. This type of technolog...

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Abstract

The present invention provides improved methods, compositions and kits for short read next generation sequencing (NGS). The methods, compositions and kits of the present invention enable phasing of two or more nucleic acid sequences in a sample, i.e. determining whether the nucleic acid sequences (typically comprising regions of sequence variation) are located on the same chromosome and/or the same chromosomal fragment. Phasing information is obtained by performing multiple, successive sequencing reactions from the same immobilized nucleic acid template. The methods, compositions and kits provided herein are useful, for example, for haplotyping, SNP phasing, or for determining downstream exons in RNA-seq.

Description

CROSS-REFERENCE[0001]This application claims the benefit of U.S. Provisional Application No. 61 / 801,600, filed Mar. 15, 2013, which application is incorporated herein by reference.BACKGROUND OF THE INVENTION[0002]Short read next generation sequencing (NGS) analysis has some limitations in both research and diagnostics. One key drawback is the problem of phasing. That is, when interrogating multiple loci of sequence variation, it is often impossible to determine which loci are co-located on the same chromosome or on the same chromosomal fragment. One example of a phasing problem occurs in diploid organisms in which two parental chromosomes, one from the mother and one from the father, are inherited, resulting in two copies of each gene (except for the genes carried on the sex chromosomes). Within each copy of the two copies of a gene in a diploid cell are regions of sequence variation, or loci, that fall within distinct sequence types known as alleles. Thus, allelic variation across ...

Claims

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Application Information

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IPC IPC(8): C12Q1/68G06F19/22G16B30/10
CPCG06F19/22C12Q1/6874G16B30/00G16B30/10
Inventor AMORESE, DOUGSCHROEDER, BENJAMIN G.SCOLNICK, JONATHAN
Owner NUGEN TECH
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