SNP discovery performance of two second-generation sequencing platforms in the NOD2 gene region

Organ transplantation has become a powerful strategy for the treatment of malignant diseases. Nevertheless, graft rejection is one of the main factors affecting graft survival after organ transplantation. Under this circumstance, the transplant-related mortality still keeps up. This invention includes the precise medication guidance of Tacrolimus (FK506) inapplicable population, against the side-effects of this drug. This invention, based on second-generation sequencing, has the advantages of relatively low cost and high sequencing throughput. During the design process, we collect the data of single nucleotide polymorphism (SNP) concerning the adverse drug reactions of Tacrolimus. Then we filter and summarize fifteen SNPs basing on importance degree (level >key enzyme>race). Thenceforth, after the process of analyzing the raw extract by operating BWA, Picard-tools, GATK, and Perl, we annotate SNPs by Annovar. Through this innovation, people can obtain further feedback on drugs that targets different genes in order to achieve the purpose of precision medication and minimizing the risks of misusing Tacrolimus.

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Second-Generation Sequencing Library Preparation:In VitroTagmentation via Transposome Insertion

Tag-Based Next Generation Sequencing ◽

10.1002/9783527644582.ch19 ◽

2012 ◽

pp. 311-321

Author(s):

Fraz Syed

Keyword(s):

Second Generation ◽

Sequencing Library ◽

Second Generation Sequencing ◽

Generation Sequencing

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A case report of the differential diagnosis of Cellulosimicrobium cellulans-infected endocarditis combined with intracranial infection by conventional blood culture and second-generation sequencing

BMC Infectious Diseases ◽

10.1186/s12879-020-05559-6 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Huifang Zhang ◽

Chunyan He ◽

Rui Tian ◽

Ruilan Wang

Keyword(s):

Second Generation ◽

Human Infection ◽

Sequencing Data ◽

Case Presentation ◽

Intracranial Infection ◽

Cellulosimicrobium Cellulans ◽

Two Samples ◽

Second Generation Sequencing ◽

Generation Sequencing

Abstract Background Cellulosimicrobium cellulans is a gram-positive filamentous bacterium found primarily in soil and sewage that rarely causes human infection, especially in previously healthy adults, but when it does, it often indicates a poor prognosis. Case presentation We report a case of endocarditis and intracranial infection caused by C. cellulans in a 52-year-old woman with normal immune function and no implants in vivo. The patient started with a febrile headache that progressed to impaired consciousness after 20 days, and she finally died after treatment with vancomycin combined with rifampicin. C. cellulans was isolated from her blood cultures for 3 consecutive days after her admission; however, there was only evidence of C. cellulans sequences for two samples in the second-generation sequencing data generated from her peripheral blood, which were ignored by the technicians. No C. cellulans bands were detected in her cerebrospinal fluid by second-generation sequencing. Conclusions Second-generation sequencing seems to have limitations for certain specific strains of bacteria.

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