Abstract:
:Next-generation sequencing (NGS) is a cost-effective technology capable of screening several genes simultaneously; however, its application in a clinical context requires an established workflow to acquire reliable sequencing results. Here, we report an optimized NGS workflow analyzing 22 lung cancer-related genes to sequence critical samples such as DNA from formalin-fixed paraffin-embedded (FFPE) blocks and circulating free DNA (cfDNA). Snap frozen and matched FFPE gDNA from 12 non-small cell lung cancer (NSCLC) patients, whose gDNA fragmentation status was previously evaluated using a multiplex PCR-based quality control, were successfully sequenced with Ion Torrent PGM™. The robust bioinformatic pipeline allowed us to correctly call both Single Nucleotide Variants (SNVs) and indels with a detection limit of 5%, achieving 100% specificity and 96% sensitivity. This workflow was also validated in 13 FFPE NSCLC biopsies. Furthermore, a specific protocol for low input gDNA capable of producing good sequencing data with high coverage, high uniformity, and a low error rate was also optimized. In conclusion, we demonstrate the feasibility of obtaining gDNA from FFPE samples suitable for NGS by performing appropriate quality controls. The optimized workflow, capable of screening low input gDNA, highlights NGS as a potential tool in the detection, disease monitoring, and treatment of NSCLC.
journal_name
Int J Mol Scijournal_title
International journal of molecular sciencesauthors
Vanni I,Coco S,Truini A,Rusmini M,Dal Bello MG,Alama A,Banelli B,Mora M,Rijavec E,Barletta G,Genova C,Biello F,Maggioni C,Grossi Fdoi
10.3390/ijms161226129subject
Has Abstractpub_date
2015-12-03 00:00:00pages
28765-82issue
12issn
1422-0067pii
ijms161226129journal_volume
16pub_type
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journal_title:International journal of molecular sciences
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journal_title:International journal of molecular sciences
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journal_title:International journal of molecular sciences
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journal_title:International journal of molecular sciences
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abstract::Phostensin is encoded by KIAA1949. 5'-RACEanalysis has been used to identify the translation start site of phostensin mRNA, indicating that it encodes 165 amino acids with an apparent molecular weight of 26 kDa on SDS-PAGE. This low-molecular-weight phostensin is present in human peripheral blood mononuclear cells and...
journal_title:International journal of molecular sciences
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journal_title:International journal of molecular sciences
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journal_title:International journal of molecular sciences
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journal_title:International journal of molecular sciences
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更新日期:2020-11-11 00:00:00
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journal_title:International journal of molecular sciences
pub_type: 杂志文章
doi:10.3390/ijms21051618
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abstract::Increasing evidence suggests that the metal homeostasis is involved in the pathogenesis of various neurodegenerative diseases including senile type of dementia such as Alzheimer's disease, dementia with Lewy bodies, and vascular dementia. In particular, synaptic Zn2+ is known to play critical roles in the pathogenesis...
journal_title:International journal of molecular sciences
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更新日期:2020-04-07 00:00:00
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journal_title:International journal of molecular sciences
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doi:10.3390/ijms18061195
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journal_title:International journal of molecular sciences
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journal_title:International journal of molecular sciences
pub_type: 杂志文章
doi:10.3390/ijms21082994
更新日期:2020-04-23 00:00:00
abstract::Hybrid magnetorheological elastomers (hMREs) were manufactured based on silicone rubber, silicone oil, carbonyl iron microparticles, graphene nanoparticles and cotton fabric. Using the hMREs, flat capacitors (FCs) were made. Using the installation described in this paper, the electrical capacitance and the coefficient...
journal_title:International journal of molecular sciences
pub_type: 杂志文章
doi:10.3390/ijms20174201
更新日期:2019-08-27 00:00:00
abstract::Human cytomegalovirus (HCMV) is an opportunistic pathogen causing disease mainly in immunocompromised patients or after congenital infection. HCMV infection of the respiratory tract leads to pneumonitis in the immunocompromised host, which is often associated with a bad clinical course. The related mouse cytomegalovir...
journal_title:International journal of molecular sciences
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journal_title:International journal of molecular sciences
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journal_title:International journal of molecular sciences
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journal_title:International journal of molecular sciences
pub_type: 杂志文章,评审
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journal_title:International journal of molecular sciences
pub_type: 杂志文章
doi:10.3390/ijms15022858
更新日期:2014-02-19 00:00:00
abstract::Diabetic nephropathy (DN) is the main cause of end-stage renal disease, which remains incurable. The progression of DN is associated with progressive and irreversible renal fibrosis and also high levels of adenosine. Our aim was to evaluate the effects of ADORA3 antagonism on renal injury in streptozotocin-induced dia...
journal_title:International journal of molecular sciences
pub_type: 杂志文章
doi:10.3390/ijms20184531
更新日期:2019-09-13 00:00:00
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journal_title:International journal of molecular sciences
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doi:10.3390/ijms20010206
更新日期:2019-01-08 00:00:00
abstract::In advanced cirrhosis, the TNFα-mediated intestinal inflammation and bacteria dysbiosis are involved in the development of inflammation and vasoconstriction-related renal dysfunction. In colitis and acute kidney injury models, activation of SIRT1 attenuates the TNFα-mediated intestinal and renal abnormalities. This st...
journal_title:International journal of molecular sciences
pub_type: 杂志文章
doi:10.3390/ijms22031233
更新日期:2021-01-27 00:00:00
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journal_title:International journal of molecular sciences
pub_type: 杂志文章
doi:10.3390/ijms21072304
更新日期:2020-03-26 00:00:00
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journal_title:International journal of molecular sciences
pub_type: 杂志文章,评审
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journal_title:International journal of molecular sciences
pub_type: 杂志文章
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abstract::In many social anxiety disorder (SAD) patients, the efficacy of antidepressant therapy is unsatisfactory. Here, we investigated whether mice deficient for the lysosomal glycoprotein acid sphingomyelinase (ASM-/-) represent an appropriate tool to study antidepressant-resistant social fear. We also investigated whether ...
journal_title:International journal of molecular sciences
pub_type: 杂志文章
doi:10.3390/ijms21218220
更新日期:2020-11-03 00:00:00