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Process for aligning targeted nucleic acid sequencing data

A target sequence and sequence technology, applied in the field of nucleic acid sequencing data for comparison and targeting, can solve problems such as hindering output, complicating workflow, and computing power requirements

Pending Publication Date: 2020-01-14
ILLUMINA INC
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

This need complicates workflow, places additional time and effort requirements on users of such methods and computer systems implementing them, and delays in analysis, and places additional demands on computing power, hampering output

Method used

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  • Process for aligning targeted nucleic acid sequencing data
  • Process for aligning targeted nucleic acid sequencing data
  • Process for aligning targeted nucleic acid sequencing data

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0103] Example 1 - Example system implementing off-target match detection

[0104] figure 1 is a block diagram of an example system 100 that implements off-target match detection for generating revised reference genome sequences from transcript sequences 180. In any instance herein, a string may take the form of a sequence of characters representing a string of values. Although referred to herein as a "string," the internal representation may take the form of a string, array, or other data structure. A character can take the form of a character or a code representing the character.

[0105] In this embodiment, a plurality of candidate primer sequences 110 are received as input by the off-target detection tool 150 . As described herein, these candidate primer sequences 110 may take the form of primer pairs that target specific positions on the transcript sequence 180 representing the plus strand of a transcript sequence transcribable from a reference genome as described he...

Embodiment 2

[0116] Example 2 - Example method for detecting off-target matches

[0117] figure 2 is a flowchart of an example method 200 of implementing off-target match detection and may be performed, for example, in a figure 1 implemented in the system shown in . Multiple candidate primer sequences targeting multiple targets on the transcript sequence can be supported.

[0118] In practice, steps can be taken, such as the use of primer generation tools, etc., to generate candidate primer sequence pairs before the method begins.

[0119] At 220, candidate primer sequences are received. Candidate primer sequences can take any form described herein.

[0120] At 230, for candidate primer sequences, matches on transcript sequences are identified. The match determination may include applying a plurality of rules as described herein. For example, multiple candidate matching conditions can be identified on the transcript sequence (eg, by means of matching rules as described herein). F...

Embodiment 3

[0127] Example 3 - Example off-target match detection

[0128] In any of the examples herein, an off-target match can take the form of a pair of candidate primer sequences (eg, from the original primer pair or two different primer pairs) that match at adjacent positions as described herein. In practice, adjacent positions may be on two different (eg, one original, one reverse complementary to the original) transcript sequences as described herein; by taking the reverse complement of the candidate primer sequence and incorporating it into the candidate Of the primer sequences, a single transcript sequence can be used to perform the calculations. Detection of such off-target matches can be used to determine whether candidate primer sequences are acceptable or unacceptable, as described herein. Candidate primer sequences (and their primer pairs) that exceed the off-target match status threshold may be considered unacceptable.

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Abstract

Provided is a computer-implemented method of aligning RNA including receiving onto a data storage unit primer sequences and transcript sequences transcribable from a reference genome based on a gene model, generating target sequences to be amplified from a combination of the primer sequences and the transcript sequences, generating a modified reference genome based on the plurality of target sequences, aligning sequence reads generated from a test sample comprising RNA amplicon molecules to the of target sequences, and generating an alignment profile for the test sample based on the aligning.Also provided is a computer system for performing the foregoing method.

Description

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS [0002] This application claims the benefit of priority to US Provisional Patent Application No. 62 / 614,088, filed January 5, 2018, the entire contents of which are incorporated herein by reference. [0003] Field of Invention [0004] The subject matter disclosed herein relates to methods and computer systems for aligning RNAs. More specifically, the present disclosure relates to aligning reads from expressed RNA to a revised reference genome comprising transcripts transcribable from the reference genome using primers according to a gene model. [0005] Background of the Invention [0006] RNA alignment involves the identification of RNA transcripts in a test sample, such as RNA produced by cells or cell populations. Standard whole-genome alignment analysis is not well suited for processing amplicon sequencing data because amplicon data contains unique primer artifacts, is subject to false positive (off-target) amplification, a...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B25/20G16B30/10
CPCG16B25/20G16B30/10G16B40/20G16B50/00
Inventor G·J·比恩J·布吕昂R·M·凯利C·李D·M·埃米格-阿希乌斯E·艾伦Y·孙
Owner ILLUMINA INC
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