bims-lifras 2024-01-28 papers

Issue of 2024–01–28
three papers selected by
Joanna Zawacka, Karolinska Institutet

Biomedicines. 2023 Dec 27. pii: 64. [Epub ahead of print]12(1):

Case Report of a DDX41 Germline Mutation in a Family with Multiple Relatives Suffering from Leukemia.

Jan Nicolai Wagner, Maximilian Al-Bazaz, Anika Forstreuter, Mohammad Ibrahim Hammada, Jurek Hille, Dzhoy Papingi, Carsten Bokemeyer, Walter Fiedler.

INTRODUCTION: Previously, it was assumed that genetic influence played a minor role in acute myeloid leukemia (AML). Increasing evidence of germline mutations has emerged, such as DDX41 germline mutation associated with familial AML.
CASE PRESENTATION: A 64-year-old male patient presented with reduced exercise tolerance and shortness of breath. Following confirmation of AML diagnosis, the patient was enrolled into the AMLSG-30-18 study with a requirement for allogenic stem cell transplantation. The sister was initially selected as a fully HLA-matched donor. However, the family history showed risks for familial AML. Due to the striking family history, further diagnostic steps were initiated to detect a germline mutation.
METHODS: Using NGS in the patients' bone marrow AML sample, a DDX41 mutation with a VAF of 49% was detected, raising the possibility of a germline mutation. DNA from cheek swabs and eyebrows were tested for the presence of the DDX41 mutation in all siblings.
RESULTS: DDX41 germline mutation was detected in 5 out of 6 siblings. The sister was excluded as a related donor and the search for an unrelated donor was initiated.
CONCLUSION: Obtaining family history of cancer patients plays a crucial role in oncology. If a germline mutation is suspected, further family work-up should be initiated.

Keywords: CPX-351; DDX41; acute leukemia; genetics; germline mutation

DOI: https://doi.org/10.3390/biomedicines12010064

Hum Mol Genet. 2024 Jan 25. pii: ddae009. [Epub ahead of print]

Challenges and approaches to calibrating patient phenotype as evidence for cancer gene variant classification under ACMG/AMP guidelines.

Cristina Fortuno, Kyriaki Michailidou, Michael Parsons, Jill S Dolinsky, Tina Pesaran, Amal Yussuf, Jessica L Mester, Kathleen S Hruska, Susan Hiraki, Robert O'Connor, Raymond C Chan, Serra Kim, Sean V Tavtigian, David Goldgar, Paul A James, Amanda B Spurdle.

Since first publication of the American College of Medical Genetics and Genomics/Association for Medical Pathology (ACMG/AMP) variant classification guidelines, additional recommendations for application of certain criteria have been released (https://clinicalgenome.org/docs/), to improve their application in the diagnostic setting. However, none have addressed use of the PS4 and PP4 criteria, capturing patient presentation as evidence towards pathogenicity. Application of PS4 can be done through traditional case-control studies, or "proband counting" within or across clinical testing cohorts. Review of the existing PS4 and PP4 specifications for Hereditary Cancer Gene Variant Curation Expert Panels revealed substantial differences in the approach to defining specifications. Using BRCA1, BRCA2 and TP53 as exemplar genes, we calibrated different methods proposed for applying the "PS4 proband counting" criterion. For each approach, we considered limitations, non-independence with other ACMG/AMP criteria, broader applicability, and variability in results for different datasets. Our findings highlight inherent overlap of proband-counting methods with ACMG/AMP frequency codes, and the importance of calibration to derive dataset-specific code weights that can account for potential between-dataset differences in ascertainment and other factors. Our work emphasizes the advantages and generalizability of logistic regression analysis over simple proband-counting approaches to empirically determine the relative predictive capacity and weight of various personal clinical features in the context of multigene panel testing, for improved variant interpretation. We also provide a general protocol, including instructions for data formatting and a web-server for analysis of personal history parameters, to facilitate dataset-specific calibration analyses required to use such data for germline variant classification.

Keywords: ACMG PS4; cancer gene; germline variant classification; logistic regression; proband counting

DOI: https://doi.org/10.1093/hmg/ddae009

Medicina (Kaunas). 2023 Dec 30. pii: 73. [Epub ahead of print]60(1):

Germline DNA Damage Response Gene Mutations in Localized Prostate Cancer.

Tomas Januskevicius, Ieva Vaicekauskaite, Rasa Sabaliauskaite, Augustinas Matulevicius, Alvydas Vezelis, Albertas Ulys, Sonata Jarmalaite, Feliksas Jankevicius.

Background and Objectives: Germline DNA damage response (DDR) gene mutations correlate with increased prostate cancer (PCa) risk and a more aggressive form of the disease. DDR mutation testing is recommended for metastatic PCa cases, while eligible information about the mutations' burden in the early-stage localized PCa is still limited. This study is aimed at the prospective detection of DDR pathway mutations in cases with localized PCa and correlation with clinical, histopathological, and radiological data. A comparison to the previously assessed cohort of the advanced PCa was performed. Materials and Methods: Germline DDR gene mutations were assessed prospectively in DNA samples from 139 patients, using a five-gene panel (BRCA1, BRCA2, ATM, CHEK2, and NBN) targeted next-generation sequencing. Results: This study revealed an almost three-fold higher risk of localized PCa among mutation carriers as compared to non-carriers (OR 2.84 and 95% CI: 0.75-20.23, p = 0.16). The prevalence of germline DDR gene mutations in PCa cases was 16.8% (18/107) and they were detected only in cases with PI-RADS 4/5 lesions. BRCA1/BRCA2/ATM mutation carriers were 2.6 times more likely to have a higher (>1) cISUP grade group compared to those with a CHEK2 mutation (p = 0.27). However, the number of cISUP > 1-grade patients with a CHEK2 mutation was significantly higher in advanced PCa than in localized PCa: 66.67% vs. 23.08% (p = 0.047). Conclusions: The results of our study suggest the potential of genetic screening for selected DDR gene mutations for early identification of cases at risk of aggressive PCa.

Keywords: DNA damage response; germline mutation; localized prostate cancer; next-generation sequencing

DOI: https://doi.org/10.3390/medicina60010073