A single-sample microarray normalization method to facilitate personalized-medicine workflows

Piccolo, Stephen R.; Sun, Ying; Campbell, Joshua D.; Lenburg, Marc E.; Bild, Andrea; Johnson, W. Evan

doi:10.1016/j.ygeno.2012.08.003

Cited by 213 publications

(192 citation statements)

References 24 publications

(30 reference statements)

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“…The expression of approximately 1.4 million PSRs was normalized and summarized using SCAN 22 to the Affymetrix core transcript cluster level (approximately 22,000 genes). Expression data were uploaded to Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo, accession number GSE72220).…”

Section: Expression Data Processing Analysismentioning

confidence: 99%

Application of a Clinical Whole-Transcriptome Assay for Staging and Prognosis of Prostate Cancer Diagnosed in Needle Core Biopsy Specimens

Knudsen

Kim

Erho

et al. 2016

The Journal of Molecular Diagnostics

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Molecular and genomic analysis of microscopic quantities of tumor from formalin-fixed, paraffin-embedded biopsy specimens has many unique challenges. Herein, we evaluated the feasibility of obtaining transcriptome-wide RNA expression to measure prognostic classifiers in diagnostic prostate needle core biopsy specimens. One-hundred fifty-eight samples from diagnostic needle core biopsy specimens (BX) and radical prostatectomies (RPs) were collected from 33 patients at three hospitals; each patient provided up to six tumor and benign samples. Genome-wide transcriptomic profiles were generated using Affymetrix Human Exon arrays for comparison of gene expression alterations and prognostic signatures between the BX and RP samples. A sufficient amount of RNA (>100 ng) was obtained from all RP specimens (n Z 77) and from 72 of 81 of BX specimens. Of transcriptomic features detected in RP, 95% were detectable in BX tissues and demonstrated a high correlation (r Z 0.96). Likewise, an expression signature pattern validated on RPs (Decipher prognostic test) showed correlation between BX and RP (r Z 0.70). Of matched BX and RP pairs, 25% showed discordant molecular subtypes. Genome-wide exon arrays yielded data of comparable quality from biopsy and RP tissues. The high concordance of tumor-associated gene expression changes between BX and RP samples provides evidence for the adequate performance of the assay platform with samples from prostate needle biopsy specimens with limited tumor volume. (J Mol Diagn 2016, 18: 395e406; http://dx

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Section: Expression Data Processing Analysismentioning

confidence: 99%

Application of a Clinical Whole-Transcriptome Assay for Staging and Prognosis of Prostate Cancer Diagnosed in Needle Core Biopsy Specimens

Knudsen

Kim

Erho

et al. 2016

The Journal of Molecular Diagnostics

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“…Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, the single-channel array normalization method can normalize each sample individually by modeling and removing probe-and array-specific background noise using only internal array data. 15 We further used the alternative CDF files from BrainArray Resource (http://brainarray. mbni.med.umich.edu/) to summarize the probe level intensities directly to the Entrez gene IDs.…”

Section: Sample Collection and Data Curationmentioning

confidence: 99%

Pan-cancer transcriptome analysis reveals a gene expression signature for the identification of tumor tissue origin

Xu¹,

Chen²,

et al. 2016

Modern Pathology

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Carcinoma of unknown primary, wherein metastatic disease is present without an identifiable primary site, accounts for~3-5% of all cancer diagnoses. Despite the development of multiple diagnostic workups, the success rate of primary site identification remains low. Determining the origin of tumor tissue is, thus, an important clinical application of molecular diagnostics. Previous studies have paved the way for gene expression-based tumor type classification. In this study, we have established a comprehensive database integrating microarray-and sequencing-based gene expression profiles of 16 674 tumor samples covering 22 common human tumor types. From this pan-cancer transcriptome database, we identified a 154-gene expression signature that discriminated the origin of tumor tissue with an overall leave-one-out cross-validation accuracy of 96.5%. The 154-gene expression signature was first validated on an independent test set consisting of 9626 primary tumors, of which 97.1% of cases were correctly classified. Furthermore, we tested the signature on a spectrum of diagnostically challenging tumors. An overall accuracy of 92% was achieved on the 1248 tumor specimens that were poorly differentiated, undifferentiated or from metastatic tumors. Thus, we have identified a 154-gene expression signature that can accurately classify a broad spectrum of tumor types. This gene panel may hold a promise to be a useful additional tool for the determination of the tumor origin.

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“…20,21 Following microarray quality control using the Affymetrix Power Tools packages, 22 probeset summarization and normalization was performed utilizing the single-channel array normalization algorithm. 23 None of these samples were used in the development of the Decipher genomic classifier. 24 Calculation of clinical and genomic risk of metastasis Clinical risk of metastatic progression was calculated with CAPRA-S score using six clinico-pathological variables as described previously.…”

Section: Specimen Collection and Handlingmentioning

confidence: 99%

Efficacy of Postoperative Radiation in a Prostatectomy Cohort Adjusted for Clinical and Genomic Risk

Den

Yousefi

Trock

et al. 2016

International Journal of Radiation Oncology*Biology*Physics

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BACKGROUND: To date, there have been no published trials examining the impact of salvage radiation therapy (SRT) in the post-operative setting for prostate cancer (PCa). We conducted a retrospective, comparative study of post-operative radiation following radical prostatectomy (RP) for men with pT3 disease or positive margins (adverse pathological features, APF). METHODS: 422 PCa men treated at four institutions with RP and having APF were analyzed with a primary end point of metastasis. Adjuvant radiation treatment (ART, n = 111), minimal residual disease (MRD) SRT (n = 70) and SRT (n = 83) were defined by PSA levels of o 0.2, 0.2-0.49 and ⩾ 0.5 ng ml − 1 , respectively, before radiation therapy (RT) initiation. Remaining 157 men who did not receive additional therapy before metastasis formed the no RT arm. Clinical-genomic risk was assessed by Cancer of the Prostate Risk Assessment Post-Surgical (CAPRA-S) and Decipher. Cox regression was used to evaluate the impact of treatment on outcome. RESULTS: During the study follow-up, 37 men developed metastasis with a median follow-up of 8 years. Both CAPRA-S and Decipher had independent predictive value on multivariable analysis for metastasis (P o0.05). Adjusting for clinical-genomic risk, SRT and no RT had hazard ratios of 4.31 (95% confidence interval, 1.20-15.47) and 5.42 (95% confidence interval, 1.59-18.44) for metastasis compared with ART, respectively. No significant difference was observed between MRD-SRT and ART (P = 0.28). Men with low-to-intermediate CAPRA-S and low Decipher value have a low rate of metastatic events regardless of treatment selection. In contrast, men with high CAPRA-S and Decipher benefit from ART, however the cumulative incidence of metastasis remains high. CONCLUSIONS: The decision as to the timing and need for additional local therapy following RP is nuanced and requires providers and patients to balance risks of morbidity with improved oncological outcomes. Post-RP treatment can be safely avoided for men who are low risk by clinical-genomic risk, whereas those at high risk should favor enrollment in clinical trials. Prostate Cancer and Prostatic Diseases INTRODUCTIONAggressive treatment approaches that have not yet been shown to improve overall survival are controversial within oncology, particularly in the management of men with prostate cancer (PCa). 1,2 Three randomized clinical trials in men with nonmetastatic PCa following surgical resection showed that treatment with adjuvant radiation therapy (ART) as compared with observation resulted in lower rates of biochemical recurrence, yet had conflicting impact on metastasis-free and overall survival. [3][4][5] Given the disparate findings, there has been an increase in utilization of salvage radiation therapy (SRT) 6 with concomitant decrease in ART, despite no randomized prospective trial evidence supporting this clinical decision. Although multiple randomized clinical trials are ongoing, 7,8 results are not expected for several years. Thus, patients and physicians are left with mu...

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A single-sample microarray normalization method to facilitate personalized-medicine workflows

Cited by 213 publications

References 24 publications

Application of a Clinical Whole-Transcriptome Assay for Staging and Prognosis of Prostate Cancer Diagnosed in Needle Core Biopsy Specimens

Application of a Clinical Whole-Transcriptome Assay for Staging and Prognosis of Prostate Cancer Diagnosed in Needle Core Biopsy Specimens

Pan-cancer transcriptome analysis reveals a gene expression signature for the identification of tumor tissue origin

Efficacy of Postoperative Radiation in a Prostatectomy Cohort Adjusted for Clinical and Genomic Risk

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