bims-ovdlit 2024-11-17 papers

Nat Methods. 2024 Nov;21(11): 1974

DOI: https://doi.org/10.1038/s41592-024-02510-4

Nat Commun. 2024 Nov 14. 15(1): 9876

Unravelling mutational signatures with plasma circulating tumour DNA.

Sebastian Hollizeck, Ning Wang, Stephen Q Wong, Cassandra Litchfield, Jerick Guinto, Sarah Ftouni, Richard Rebello, Sehrish Kanwal, Ruining Dong, Sean Grimmond, Shahneen Sandhu, Linda Mileshkin, Richard W Tothill, Dineika Chandrananda, Sarah-Jane Dawson.

The use of circulating tumour DNA (ctDNA) to profile mutational signatures represents a non-invasive opportunity for understanding cancer mutational processes. Here we present MisMatchFinder, a liquid biopsy approach for mutational signature detection using low-coverage whole-genome sequencing of ctDNA. Through analysis of 375 plasma samples across 9 cancers, we demonstrate that MisMatchFinder accurately infers single-base and doublet-base substitutions, as well as insertions and deletions to enhance the detection of ctDNA and clinically relevant mutational signatures.

DOI: https://doi.org/10.1038/s41467-024-54193-2

Obstet Gynecol. 2024 Nov 07.

Optimization of Timing for Risk-Reducing Salpingectomy and Oophorectomy.

Kathryn P Pennington, Stephanie L Pugh, Warner Huh, Joan L Walker, Elizabeth Jewell, Laura J Havrilesky, Jeanne Carter, Carolyn Y Muller, Ronny Drapkin, Heather A Lankes, Tara Castellano, Abigail S Zamorano, Stephanie V Blank, Lisa A Kachnic.

CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, NCT04251052.

DOI: https://doi.org/10.1097/AOG.0000000000005781

Fam Cancer. 2024 Nov 15. 24(1): 4

BRCAIndica: a resource for ACMG/AMP classified BRCA1 and BRCA2 variants.

Aastha Vatsyayan, R I Anu, Prerika Mathur, Divya Uchil, Ashish Joshi, Aradhana Dwivedi, Bhawna Sirohi, Aju Mathew, Dileep Damodaran, Soumya Surath Panda, Spoorthy Kolluri, Shaji K Ayillath, Deepak Amalnath, Gomathi Shankar, Kavita Pandhare, Vinod Scaria.

As genetic testing becomes increasingly accessible and affordable, the uniform and accurate interpretation of genetic variants becomes essential. The ACMG/AMP joint guidelines provide the basis for systematic and uniform interpretation of pathogenicity of genetic variants. However, the application of these in routine clinical interpretation at-scale has largely been limited by the lack of resources providing harmonized data especially at a population-scale. Here we describe BRCAIndica, a resource for BRCA1 and BRCA2 variants conforming to the ACMG & AMP joint guidelines to aid uniform clinical interpretation of genetic tests with a specific focus on variants reported in the Indian population. We collected and harmonized variants from across several resources including population-scale datasets, literature survey and other variant datasets. We then classified them according to the ACMG/AMP guidelines.We have collected a total of 10,490 unique variants, of which 2261 Pathogenic and 43 Likely Pathogenic variants belong to BRCA1 and 2694 Pathogenic and 20 Likely Pathogenic variants to BRCA2 respectively. BRCAIndica can be accessed at:https://clingen.igib.res.in/brcaindica/ . In conclusion, BRCAIndica is a powerful resource that offers researchers and clinicians with ACMG/AMP annotated BRCA variants.

Keywords: ACMG; Cancer prevention; Database; Oncogenomics; Precision oncology

DOI: https://doi.org/10.1007/s10689-024-00429-5

JCO Oncol Pract. 2024 Nov;20(11): 1491-1499

Cell-Free DNA in Hematologic Malignancies.

Joseph G Schroers-Martin, Ash A Alizadeh.

Liquid biopsy techniques using cell-free DNA (cfDNA) play an increasingly important role in the characterization and surveillance of solid tumors. For blood cancers, molecular response assessment techniques using circulating malignant cells or bone marrow aspirates are well established in clinical care. However, cfDNA has an emerging role in hematology as well, with the opportunity for disease assessment and quantification independent of circulating disease burden or invasive biopsies. In this review, we discuss key technologies and clinical data for the utilization of cfDNA in lymphomas, myeloma, and leukemias.

DOI: https://doi.org/10.1200/OP-24-00648