Abstract:
:Background: To support cancer therapy, development of low cost library preparation techniques for targeted next generation sequencing (NGS) is needed. In this study we designed and tested a PCR-based library preparation panel with limited target area for sequencing the top 12 somatic mutation hot spots in colorectal cancer on the GS Junior instrument. Materials and Methods: A multiplex PCR panel was designed to amplify regions of mutation hot spots in 12 selected genes (APC, BRAF, CTNNB1, EGFR, FBXW7, KRAS, NRAS, MSH6, PIK3CA, SMAD2, SMAD4, TP53). Amplicons were sequenced on a GS Junior instrument using ligated and barcoded adaptors. Eight samples were sequenced in a single run. Colonic DNA samples (8 normal mucosa; 33 adenomas; 17 adenocarcinomas) as well as HT-29 and Caco-2 cell lines with known mutation profiles were analyzed. Variants found by the panel on APC, BRAF, KRAS and NRAS genes were validated by conventional sequencing. Results: In total, 34 kinds of mutations were detected including two novel mutations (FBXW7 c.1740:C>G and SMAD4 c.413C>G) that have not been recorded in mutation databases, and one potential germline mutation (APC). The most frequently mutated genes were APC, TP53 and KRAS with 30%, 15% and 21% frequencies in adenomas and 29%, 53% and 29% frequencies in carcinomas, respectively. In cell lines, all the expected mutations were detected except for one located in a homopolymer region. According to re-sequencing results sensitivity and specificity was 100% and 92% respectively. Conclusions: Our NGS-based screening panel denotes a promising step towards low cost colorectal cancer genotyping on the GS Junior instrument. Despite the relatively low coverage, we discovered two novel mutations and obtained mutation frequencies comparable to literature data. Additionally, as an advantage, this panel requires less template DNA than sequence capture colon cancer panels currently available for the GS Junior instrument.
journal_name
J Cancerjournal_title
Journal of Cancerauthors
Péterfia B,Kalmár A,Patai ÁV,Csabai I,Bodor A,Micsik T,Wichmann B,Egedi K,Hollósi P,Kovalszky I,Tulassay Z,Molnár Bdoi
10.7150/jca.16037subject
Has Abstractpub_date
2017-01-12 00:00:00pages
162-173issue
2issn
1837-9664pii
jcav08p0162journal_volume
8pub_type
杂志文章abstract::Hepatocellular carcinoma (HCC) is the sixth most common tumor worldwide. The relationship between the gene methylation accumulation and HCC has been widely studied. In our study, we used the Sequenom EpiTYPER assay to investigate the methylation levels of the RASA3 in 164 HCC samples and paired adjacent non-cancerous ...
journal_title:Journal of Cancer
pub_type: 杂志文章
doi:10.7150/jca.24567
更新日期:2018-05-25 00:00:00
abstract::Background: Heavy metal pollution in farm soils is a grave concern in Taiwan. Previously, we found the incidence of oral cancer (OC) correlated positively with levels of nickel and arsenic in farm soils. Many OC patients have a second malignancy, among which esophageal cancer (EC) is the most common one in Taiwan. Obj...
journal_title:Journal of Cancer
pub_type: 杂志文章
doi:10.7150/jca.15441
更新日期:2016-08-06 00:00:00
abstract::Melanoma is the most aggressive and treatment-resistant form of skin cancer. Curcumol is a Chinese medicinal herb traditionally used as a cancer remedy. However, the molecular mechanisms underlying the anticancer activity of curcumol in melanoma remains largely unknown. In the present study, we observed that Curcumol ...
journal_title:Journal of Cancer
pub_type: 杂志文章
doi:10.7150/jca.38624
更新日期:2020-01-14 00:00:00
abstract::Nasopharyngeal carcinoma (NPC), is one of the most common malignant tumor in southern China and southeast Asia. MYH10 is a coding gene of the NMMHC-IIB protein. Previous studies have shown that MYH10 expression was up-regulated in breast cancer, glioma and meningioma. Moreover, it was targeted by miR200 family. Howeve...
journal_title:Journal of Cancer
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abstract::Objectives: PD-1 and PD-L1 overexpression in malignant tumors in response to radiotherapy is correlated with a poor prognosis. Human papilloma virus (HPV) infection impacts intrinsic radiosensitivity of head and neck cancers (HNCs). Herein, this study aims to determine PD-1/PD-L1 expression differences in tumors with ...
journal_title:Journal of Cancer
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doi:10.7150/jca.27199
更新日期:2019-01-29 00:00:00
abstract::We discuss the hypothesis that ZEB1-Wnt-p300 signaling integrates epithelial to mesenchymal transition (EMT) and resistance to histone deacetylase inhibitors (HDACis) in colorectal cancer (CRC) cells. The HDACi butyrate, derived from dietary fiber, has been linked to CRC prevention, and other HDACis have been proposed...
journal_title:Journal of Cancer
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更新日期:2017-05-12 00:00:00
abstract::Hedgehog (Hh) signalling plays an important role in cancer; however, its mechanism in ovarian cancer migration and invasion remains unclear. In the present study, we aimed to clarify the effect of the Hh signalling pathway on ovarian cancer migration and invasion through the regulation of CD24 expression, both in vitr...
journal_title:Journal of Cancer
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更新日期:2017-02-25 00:00:00
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pub_type: 杂志文章,评审
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更新日期:2015-05-12 00:00:00
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doi:10.7150/jca.41415
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journal_title:Journal of Cancer
pub_type: 杂志文章
doi:10.7150/jca.2.458
更新日期:2011-01-01 00:00:00
abstract::Many preclinical and clinical studies are currently evaluating metformin in combination with classical therapeutic agents as anti-cancer therapy. In this study we used three distinct pancreatic cancer cell lines and evaluated cell death by trypan blue assay and Western Blots using antibodies directed against cleaved c...
journal_title:Journal of Cancer
pub_type: 杂志文章
doi:10.7150/jca.17972
更新日期:2017-07-01 00:00:00
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journal_title:Journal of Cancer
pub_type: 杂志文章
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更新日期:2019-07-10 00:00:00
abstract:BACKGROUND:The 2010 guidelines by ASCO-CAP have mandated that breast cancer specimens with ≥1% positively staining cells by immunohistochemistry should be considered Estrogen Receptor (ER) positive. This has led to a subclass of low-ER positive (1-10%) breast cancers. We have examined the biology and clinical behavior ...
journal_title:Journal of Cancer
pub_type: 杂志文章
doi:10.7150/jca.7668
更新日期:2014-01-23 00:00:00
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journal_title:Journal of Cancer
pub_type: 杂志文章
doi:10.7150/jca.20643
更新日期:2018-02-01 00:00:00
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journal_title:Journal of Cancer
pub_type: 杂志文章
doi:10.7150/jca.34859
更新日期:2019-10-17 00:00:00
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journal_title:Journal of Cancer
pub_type: 杂志文章
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更新日期:2015-08-20 00:00:00
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doi:10.7150/jca.20935
更新日期:2017-10-17 00:00:00
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更新日期:2017-07-21 00:00:00
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pub_type: 杂志文章
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更新日期:2015-10-25 00:00:00
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更新日期:2018-02-12 00:00:00
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