A protocol for representative sampling of solid tumors to improve the accuracy of sequencing results

Gallegos, Lisa L.; Gilchrist, Ashley; Spain, Lavinia; Stanislaw, Stacey; Hill, Samantha M.; Primus, V.; Jones, Carol; Agrawal, Somya; Tippu, Zayd; Barhoumi, Aoune; Noel-Storr, Glenn; Alexander, Nelson R.; Turajlic, Samra

doi:10.1016/j.xpro.2021.100624

Cited by 5 publications

(4 citation statements)

References 3 publications

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“…The main limitations stem from the challenges of measuring and standardizing thresholds, as well as their lack of specificity and sensitivity. On the other hand, tumor tissue sampling, while less palatable and conforming to patients’ preferences, serves as the gold standard for diagnosis by pathologists worldwide and since extraction comes from the primary site of cancer, the amount of confounding variables is reduced [ 33 , 35 , 36 , 37 ].…”

Section: Metabolomics: a Tool Against Cancermentioning

confidence: 99%

Metabolomic-Based Approaches for Endometrial Cancer Diagnosis and Prognosis: A Review

Albertí-Valls,

Megino-Luque,

Macià

et al. 2023

Cancers

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Endometrial cancer, the most prevalent gynecological malignancy in developed countries, is experiencing a sustained rise in both its incidence and mortality rates, primarily attributed to extended life expectancy and lifestyle factors. Currently, the absence of precise diagnostic tools hampers the effective management of the expanding population of women at risk of developing this disease. Furthermore, patients diagnosed with endometrial cancer require precise risk stratification to align with optimal treatment planning. Metabolomics technology offers a unique insight into the molecular landscape of endometrial cancer, providing a promising approach to address these unmet needs. This comprehensive literature review initiates with an overview of metabolomic technologies and their intrinsic workflow components, aiming to establish a fundamental understanding for the readers. Subsequently, a detailed exploration of the existing body of research is undertaken with the objective of identifying metabolite biomarkers capable of enhancing current strategies for endometrial cancer diagnosis, prognosis, and recurrence monitoring. Metabolomics holds vast potential to revolutionize the management of endometrial cancer by providing accuracy and valuable insights into crucial aspects.

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Section: Metabolomics: a Tool Against Cancermentioning

confidence: 99%

Metabolomic-Based Approaches for Endometrial Cancer Diagnosis and Prognosis: A Review

Albertí-Valls,

Megino-Luque,

Macià

et al. 2023

Cancers

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“…Another attempt to improve genomic ITH detection in solid tumors has recently been made [ 22 ]. This method proposes the homogenization of the leftover residual tumor tissue before sequencing, thus guaranteeing the full genomic analysis of the whole tumor.…”

Section: Homogenization Of the Residual Tumor Tissuementioning

confidence: 99%

“…In a context of high diagnostic pressure, some pathologists may be reluctant to increase the time and cost needed to implement both 3D fusion [ 20 ] and the homogenization of the leftover residual tumor [ 22 ], a point that may limit their widespread implementation. By contrast, MSTS saves time because it is an all-in-one procedure, enabling at the same time the histological analysis with a genomic correlation to take place in the same paraffin block and preserving the formalin-fixed paraffin-embedded material for the future.…”

Section: Homogenization Of the Residual Tumor Tissuementioning

confidence: 99%

Towards Personalized Sampling in Clear Cell Renal Cell Carcinomas

Manini

López-Fernández

López

2022

Cancers

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Intratumor heterogeneity (ITH) is a constant evolutionary event in all malignant tumors, and clear cell renal cell carcinoma (CCRCC) is a paradigmatic example. ITH is responsible for most therapeutic failures in the era of precision oncology, so its precise detection remains a must in modern medicine. Unfortunately, classic sampling protocols do not resolve the problem as expected and several strategies have been being implemented in recent years to improve such detection. Basically, multisite tumor sampling (MSTS) and the homogenization of the residual tumor tissue are on display. A next step of the MSTS strategy considering the recently discovered patterns of ITH regionalization is presented here, the so-called personalized MSTS (pMSTS). This modification consists of paying more attention to sample the tumor periphery since it is this area with maximum levels of ITH.

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“…While increasingly promising, this approach is still limited in sensitivity especially in certain cancer settings [22]. We recently described a novel tumour sampling methodology to address both under-sampling and the spatial sampling bias in current molecular profiling approaches [19,23]. This method, called "representative sequencing" (Rep-Seq) includes homogenization of residual fixed surgical tumour tissue into a well-mixed solution, followed by sequencing.…”

Section: Towards Representative Samplingmentioning

confidence: 99%