bims-ovdlit Biomed News
on Ovarian cancer: early diagnosis, liquid biopsy and therapy
Issue of 2022‒03‒20
seven papers selected by
Lara Paracchini
Humanitas Research
  1. Massively parallel enrichment of low-frequency alleles enables duplex sequencing at low depth.
  2. Cracking the homologous recombination deficiency code: how to identify responders to PARP inhibitors.
  3. Rucaparib for BRCA1/2-mutated pretreated ovarian cancer: reflections from the ARIEL4 trial.
  4. Single-cell sequencing.
  5. Early detection of cancer.
  6. Silent mutations make noise.
  7. The future of research collaborations involving Russia.
  1. Nat Biomed Eng. 2022 Mar 17.
    Massively parallel enrichment of low-frequency alleles enables duplex sequencing at low depth.
    Gregory Gydush, Erica Nguyen, Jin H Bae, Timothy Blewett, Justin Rhoades, Sarah C Reed, Douglas Shea, Kan Xiong, Ruolin Liu, Fangyan Yu, Ka Wai Leong, Atish D Choudhury, Daniel G Stover, Sara M Tolaney, Ian E Krop, J Christopher Love, Heather A Parsons, G Mike Makrigiorgos, Todd R Golub, Viktor A Adalsteinsson.
      Assaying for large numbers of low-frequency mutations requires sequencing at extremely high depth and accuracy. Increasing sequencing depth aids the detection of low-frequency mutations yet limits the number of loci that can be simultaneously probed. Here we report a method for the accurate tracking of thousands of distinct mutations that requires substantially fewer reads per locus than conventional hybrid-capture duplex sequencing. The method, which we named MAESTRO (for minor-allele-enriched sequencing through recognition oligonucleotides), combines massively parallel mutation enrichment with duplex sequencing to track up to 10,000 low-frequency mutations, with up to 100-fold fewer reads per locus. We show that MAESTRO can be used to test for chimaerism by tracking donor-exclusive single-nucleotide polymorphisms in sheared genomic DNA from human cell lines, to validate whole-exome sequencing and whole-genome sequencing for the detection of mutations in breast-tumour samples from 16 patients, and to monitor the patients for minimal residual disease via the analysis of cell-free DNA from liquid biopsies. MAESTRO improves the breadth, depth, accuracy and efficiency of mutation testing by sequencing.
    DOI:  https://doi.org/10.1038/s41551-022-00855-9
  2. Eur J Cancer. 2022 Mar 10. pii: S0959-8049(22)00070-3. [Epub ahead of print]166 87-99
    Cracking the homologous recombination deficiency code: how to identify responders to PARP inhibitors.
    Lola Paulet, Alexis Trecourt, Alexandra Leary, Julien Peron, Françoise Descotes, Mojgan Devouassoux-Shisheboran, Karen Leroy, Benoit You, Jonathan Lopez.
      DNA double-strand breaks are the most critical DNA damage to cells, and their repair is tightly regulated to maintain cellular integrity. Some cancers exhibit homologous recombination deficiency (HRD), a faithful double-strand break repair system, making them more sensitive to poly (ADP ribose) polymerase inhibitors (PARPi). PARPi have shown substantial efficacy in BRCA-mutated ovarian cancer for several years, and their indication has gradually been extended to other tumour locations such as breast, prostate and pancreas. More recently, PARPi were demonstrated to be effective in cancers with an HRD phenotype beyond BRCA mutations. Today, a major challenge is developing tests capable of detecting the HRD phenotype of cancers (HRD tests) and predicting sensitivity to PARPi to select patients likely to benefit from this therapy. This review provides a synthesis of the existing HRD tests, divided into three main approaches to detect HRD: the investigation of the HRD causes, the study of its consequences and the evaluation of the HR activity itself.
    Keywords:  BRCA; Genomic scars; HRD tests; Homologous recombination deficiency; PARP inhibitors; RAD51 foci
    DOI:  https://doi.org/10.1016/j.ejca.2022.01.037
  3. Lancet Oncol. 2022 Mar 14. pii: S1470-2045(22)00150-4. [Epub ahead of print]
    Rucaparib for BRCA1/2-mutated pretreated ovarian cancer: reflections from the ARIEL4 trial.
    Dearbhaile M O'Donnell.
      
    DOI:  https://doi.org/10.1016/S1470-2045(22)00150-4
  4. Nat Biotechnol. 2022 Mar;40(3): 303
    Single-cell sequencing.
      
    DOI:  https://doi.org/10.1038/s41587-022-01262-w
  5. Science. 2022 Mar 18. 375(6586): eaay9040
    Early detection of cancer.
    David Crosby, Sangeeta Bhatia, Kevin M Brindle, Lisa M Coussens, Caroline Dive, Mark Emberton, Sadik Esener, Rebecca C Fitzgerald, Sanjiv S Gambhir, Peter Kuhn, Timothy R Rebbeck, Shankar Balasubramanian.
      Survival improves when cancer is detected early. However, ~50% of cancers are at an advanced stage when diagnosed. Early detection of cancer or precancerous change allows early intervention to try to slow or prevent cancer development and lethality. To achieve early detection of all cancers, numerous challenges must be overcome. It is vital to better understand who is at greatest risk of developing cancer. We also need to elucidate the biology and trajectory of precancer and early cancer to identify consequential disease that requires intervention. Insights must be translated into sensitive and specific early detection technologies and be appropriately evaluated to support practical clinical implementation. Interdisciplinary collaboration is key; advances in technology and biological understanding highlight that it is time to accelerate early detection research and transform cancer survival.
    DOI:  https://doi.org/10.1126/science.aay9040
  6. Nat Rev Cancer. 2022 Mar 17.
    Silent mutations make noise.
    Sarah Seton-Rogers.
      
    DOI:  https://doi.org/10.1038/s41568-022-00469-y
  7. Nature. 2022 Mar 18.
    The future of research collaborations involving Russia.
    Benjamin Plackett.
      
    Keywords:  Careers; Government; History; Politics; Society
    DOI:  https://doi.org/10.1038/d41586-022-00761-9
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