High-throughput genotyping system as a robust and useful tool in oncology: Experience from a single institution

Henríquez-Hernández, Luis Alberto; Valenciano, A.; Herrera-Ramos, Estefanía; Lloret, M.; Riveros-Pérez, A.; Lara, Pedro C.

doi:10.1016/j.biologicals.2013.09.006

Cited by 9 publications

(7 citation statements)

References 19 publications

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“…The SNP genotyping was performed in a Biotrove OpenArray® NT Cycler (Applied Biosystems, Foster City, CA) [ 13 ]. DNA samples loaded in the OpenArray (OA) had a A260/A280 and A260/230 ratios of 1.7-1.9, and were adjusted to 50 ng/μl.…”

Section: Methodsmentioning

confidence: 99%

Single nucleotide polymorphisms in DNA repair genes as risk factors associated to prostate cancer progression

et al. 2014

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BackgroundBesides serum levels of PSA, there is a lack of prostate cancer specific biomarkers. It is need to develop new biological markers associated with the tumor behavior which would be valuable to better individualize treatment. The aim of this study was to elucidate the relationship between single nucleotide polymorphisms (SNPs) in genes involved in DNA repair and prostate cancer progression.MethodsA total of 494 prostate cancer patients from a Spanish multicenter study were genotyped for 10 SNPs in XRCC1, ERCC2, ERCC1, LIG4, ATM and TP53 genes. The SNP genotyping was made in a Biotrove OpenArray® NT Cycler. Clinical tumor stage, diagnostic PSA serum levels, and Gleason score at diagnosis were obtained for all participants. Genotypic and allelic frequencies were determined using the web-based environment SNPator.ResultsSNPs rs11615 (ERCC1) and rs17503908 (ATM) appeared as risk factors for prostate cancer aggressiveness. Patients wild homozygous for these SNPs (AA and TT, respectively) were at higher risk for developing cT2b – cT4 (OR = 2.21 (confidence interval (CI) 95% 1.47 – 3.31), p < 0.001) and Gleason scores ≥ 7 (OR = 2.22 (CI 95% 1.38 – 3.57), p < 0.001), respectively. Moreover, those patients wild homozygous for both SNPs had the greatest risk of presenting D’Amico high-risk tumors (OR = 2.57 (CI 95% 1.28 – 5.16)).ConclusionsGenetic variants at DNA repair genes are associated with prostate cancer progression, and would be taken into account when assessing the malignancy of prostate cancer.Electronic supplementary materialThe online version of this article (doi:10.1186/s12881-014-0143-0) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Single nucleotide polymorphisms in DNA repair genes as risk factors associated to prostate cancer progression

et al. 2014

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“…Here we report the discovery and characterization of a 29-gene panel in PBMC for the detection of colorectal adenomas and carcinomas using a nanoliter high throughput qPCR platform (OpenArray) [ 22 ]. To this purpose we used samples prospectively collected from a multicenter, case-control study in which patients were referred for colonoscopy or scheduled for surgery for CRC removal.…”

Section: Introductionmentioning

confidence: 99%

Discovery of a 29-Gene Panel in Peripheral Blood Mononuclear Cells for the Detection of Colorectal Cancer and Adenomas Using High Throughput Real-Time PCR

Ciarloni¹,

Hosseinian²,

Monnier-Benoit³

et al. 2015

PLoS ONE

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Colorectal cancer (CRC) is the second leading cause of cancer-related death in developed countries. Early detection of CRC leads to decreased CRC mortality. A blood-based CRC screening test is highly desirable due to limited invasiveness and high acceptance rate among patients compared to currently used fecal occult blood testing and colonoscopy. Here we describe the discovery and validation of a 29-gene panel in peripheral blood mononuclear cells (PBMC) for the detection of CRC and adenomatous polyps (AP). Blood samples were prospectively collected from a multicenter, case-control clinical study. First, we profiled 93 samples with 667 candidate and 3 reference genes by high throughput real-time PCR (OpenArray system). After analysis, 160 genes were retained and tested again on 51 additional samples. Low expressed and unstable genes were discarded resulting in a final dataset of 144 samples profiled with 140 genes. To define which genes, alone or in combinations had the highest potential to discriminate AP and/or CRC from controls, data were analyzed by a combination of univariate and multivariate methods. A list of 29 potentially discriminant genes was compiled and evaluated for its predictive accuracy by penalized logistic regression and bootstrap. This method discriminated AP >1cm and CRC from controls with a sensitivity of 59% and 75%, respectively, with 91% specificity. The behavior of the 29-gene panel was validated with a LightCycler 480 real-time PCR platform, commonly adopted by clinical laboratories. In this work we identified a 29-gene panel expressed in PBMC that can be used for developing a novel minimally-invasive test for accurate detection of AP and CRC using a standard real-time PCR platform.

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“…The SNP genotyping was performed in a Biotrove OpenArray NT Cycler (Applied Biosystems, Foster City, CA) [19]. DNA samples loaded in OpenArray had A260/ A280 and A260/230 ratios of 1.7 to 1.9 and were adjusted to 50 ng/ml.…”

Section: Genotypingmentioning

confidence: 99%

Genetic variations in genes involved in testosterone metabolism are associated with prostate cancer progression: A Spanish multicenter study

Henríquez-Hernández

Valenciano

Arnalot

et al. 2015

Urologic Oncology: Seminars and Original Investigations

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High-throughput genotyping system as a robust and useful tool in oncology: Experience from a single institution

Cited by 9 publications

References 19 publications

Single nucleotide polymorphisms in DNA repair genes as risk factors associated to prostate cancer progression

Single nucleotide polymorphisms in DNA repair genes as risk factors associated to prostate cancer progression

Discovery of a 29-Gene Panel in Peripheral Blood Mononuclear Cells for the Detection of Colorectal Cancer and Adenomas Using High Throughput Real-Time PCR

Genetic variations in genes involved in testosterone metabolism are associated with prostate cancer progression: A Spanish multicenter study

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