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Journal articles on the topic 'Germline Genetic Variants'

Author: Grafiati

Published: 9 September 2021

Last updated: 29 July 2025

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1

Khanna, Shivani, Steven Brad Maron, Leah Chase, Samantha Lomnicki, Sonia Kupfer, and Daniel V. T. Catenacci. "Suspected and confirmed germline variants from tumor-only somatic sequencing of 864 gastrointestinal malignancies." Journal of Clinical Oncology 37, no. 15_suppl (2019): e13131-e13131. http://dx.doi.org/10.1200/jco.2019.37.15_suppl.e13131.

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e13131 Background: Targeted tumor-only somatic sequencing informs therapies and is becoming a routine part of cancer care. It also identifies patients with possible germline variants who require confirmatory genetic testing. The aim was to identify patients with suspected and confirmed germline variants whose GI tumors underwent somatic sequencing. Methods: 864 patients with GI tumors who had Foundation One (FO) somatic sequencing from 4/2003-3/2018 were evaluated. Inclusion criteria for suspected germline variants were: a) allele frequency ≥ 35% in hereditary cancer genes and b) pathogenic va

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Bokor, Barbara Anna, Aliasgari Abdolreza, Flóra Kaptás, et al. "Novel FANCI and RAD54B Variants and the Observed Clinical Outcomes in a Hungarian Melanoma Cohort." International Journal of Molecular Sciences 26, no. 1 (2024): 23. https://doi.org/10.3390/ijms26010023.

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Accumulating evidence suggests that inherited melanoma is not rare and approx. one in seven individuals with melanoma has clinically relevant hereditable cancer-predisposing and/or -susceptibility variant(s). Concerning its germline genetic background, genetic screening aims to identify either variants of predisposing genes with high penetrance or variants of susceptibility genes with medium or low penetrance. However, less attention is paid to genetic testing of germline variants of genes influencing patients’ survival outcomes or enhancing the design of new therapies. We aimed to investigate

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Michalski, Scott T., Daniel Esteban Pineda Alvarez, Meaghan Russell, Shan Yang, Guru Sonpavde, and Edward D. Esplin. "Tumor sequencing with germline genetic testing: Identification of patients with hereditary cancer and precision treatment eligibility." Journal of Clinical Oncology 37, no. 15_suppl (2019): 1580. http://dx.doi.org/10.1200/jco.2019.37.15_suppl.1580.

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1580 Background: Cancer is a fundamentally genetic disease, as such, somatic and germline mutation analysis is used in the comprehensive assessment of patients with cancer. Studies report that approximately 10% of patient’s tumors have clinically significant variants known to predispose to hereditary cancer, with medical implications for both patients and family members. We retrospectively reviewed a series of patients where providers suspected a somatic variant also existed in the germline and followed up with clinical germline genetic testing. We report the rate of concordance between germli

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Harmon, Lauren, Zachary S. Hattig, Yizhou Peter Huang, et al. "Germline Variant Burden Warrants Universal Genetic Testing in Pediatric AML." Blood 144, Supplement 1 (2024): 4092. https://doi.org/10.1182/blood-2024-210515.

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Acute myeloid leukemia (AML) is the most lethal of pediatric leukemias. Due to its rarity, the contribution of germline genetics to pediatric AML etiology is poorly understood. Here we investigated deleterious germline variants in the largest whole-genome sequenced (WGS) pediatric AML cohort to date, combining TARGET-21 (N=29) and COG-AAML1031 (N=336) for a total of 365 patients. WGS data from 29 subjects included non-hematopoietic fibroblasts expanded from marrow; 336 subjects had matched diagnosis/remission/relapse marrow samples. Variants were considered likely germline if present at varian

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Ricker, Charité, Erika Amundson, Sandra Algaze, et al. "Assessing somatic and germline variants in cancer patients." Journal of Clinical Oncology 39, no. 15_suppl (2021): 10601. http://dx.doi.org/10.1200/jco.2021.39.15_suppl.10601.

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10601 Background: The increasing integration of somatic and germline testing into oncology practice allows physicians to target oncologic therapy and identify those with cancer predisposition. We explored the impact of a somatic assay (liquid biopsy, LB) on the identification of patients appropriate for germline genetic testing. Methods: We identified a cohort of diverse cancer patients with LB to assess for targetable somatic gene variants at LAC+USC Medical Center between 2016 and 2020 (n= 467). To enrich the cohort for variants that may reflect germline findings, we focused on the 46 patien

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Nitschke, Nikolaj Juul, Marwa Almosailleakh, Yiyuan Niu, et al. "Frequency and Functional Characterization of RUNX1 Germline Variants in Myeloid Neoplasms." Human Mutation 2023 (June 2, 2023): 1–11. http://dx.doi.org/10.1155/2023/4738660.

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Current estimates suggest that up to 10% of patients with myeloid neoplasms (MN) harbor variants associated with a germline predisposition. A pathogenic variant in the runt-related transcription factor 1 gene (RUNX1) is a frequent cause of germline predisposition to MN. RUNX1 variants detected in tumor tissue at a VAF close to 50% are potentially germline and causative of RUNX1 familial platelet disorder with associated myeloid malignancies. Previous studies have found germline RUNX1 variants in 3% of patients with acute myeloid leukemia; however, the frequency of germline RUNX1 variants in le

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Spurdle, Amanda B., Stephanie Greville-Heygate, Antonis C. Antoniou, et al. "Towards controlled terminology for reporting germline cancer susceptibility variants: an ENIGMA report." Journal of Medical Genetics 56, no. 6 (2019): 347–57. http://dx.doi.org/10.1136/jmedgenet-2018-105872.

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The vocabulary currently used to describe genetic variants and their consequences reflects many years of studying and discovering monogenic disease with high penetrance. With the recent rapid expansion of genetic testing brought about by wide availability of high-throughput massively parallel sequencing platforms, accurate variant interpretation has become a major issue. The vocabulary used to describe single genetic variants in silico, in vitro, in vivo and as a contributor to human disease uses terms in common, but the meaning is not necessarily shared across all these contexts. In the setti

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dos Santos, Wellington, Edilene Santos de Andrade, Felipe Antonio de Oliveira Garcia, et al. "Whole-Exome Sequencing Identifies Pathogenic Germline Variants in Patients with Lynch-Like Syndrome." Cancers 14, no. 17 (2022): 4233. http://dx.doi.org/10.3390/cancers14174233.

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Lynch syndrome (LS) is the most common hereditary colorectal cancer (CRC) syndrome, characterized by germline pathogenic variants in mismatch repair (MMR)-related genes that lead to microsatellite instability. Patients who meet the clinical criteria for LS and MMR deficiency and without any identified germline pathogenic variants are frequently considered to have Lynch-like syndrome (LLS). These patients have a higher risk of CRC and extracolonic tumors, and little is known about their underlying genetic causes. We investigated the germline spectrum of LLS patients through whole-exome sequenci

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Cherbal, Farid, Asma-Lamia Boumehdi, Feriel Khider, et al. "Abstract 4177: Genetic testing for hereditary colorectal cancer syndromes in Algerian patients: A multicenter study." Cancer Research 83, no. 7_Supplement (2023): 4177. http://dx.doi.org/10.1158/1538-7445.am2023-4177.

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Abstract Background To date, 5% to 6 % of all colorectal cancers (CRCs) are associated with germline pathogenic variants in cancer predisposition genes that confer inherited predisposition to CRC. The use of genetic testing to identify individuals at risk for hereditary CRC syndromes can help to prevent the development of cancer and in the clinical management of the colorectal patients in the areas of both prevention and treatment. We report here the experience of our research laboratory of genetic testing for hereditary polyposis syndromes and Lynch syndrome (LS), respectively, in 126 patient

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Aldubayan, Saud H., Jake Conway, Leora Witkowski, et al. "Expanding the diagnostic yield of germline genetic testing in cancer patients using deep learning." Journal of Clinical Oncology 38, no. 15_suppl (2020): 1518. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.1518.

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1518 Background: Germline genetic analysis is an essential tool for implementing precision cancer prevention and treatment. However, only a small fraction of cancer patients, even those with features suggestive of a cancer-predisposition syndrome, have detectable pathogenic germline events, which may in part reflect incomplete pathogenic variant detection by current gold-standard methods. Here, we leveraged deep learning approaches to expand the diagnostic utility of genetic analysis in cancer patients. Methods: Systematic analysis of the detection rate of pathogenic cancer-predisposition vari

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Forte, Giovanna, Antonia Lucia Buonadonna, Candida Fasano, et al. "Clinical and Molecular Characterization of SMAD4 Splicing Variants in Patients with Juvenile Polyposis Syndrome." International Journal of Molecular Sciences 25, no. 14 (2024): 7939. http://dx.doi.org/10.3390/ijms25147939.

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Juvenile polyposis syndrome (JPS) is an inherited autosomal dominant condition that predisposes to the development of juvenile polyps throughout the gastrointestinal (GI) tract, and it poses an increased risk of GI malignancy. Germline causative variants were identified in the SMAD4 gene in a subset (20%) of JPS cases. Most SMAD4 germline genetic variants published to date are missense, nonsense, and frameshift mutations. SMAD4 germline alterations predicted to result in aberrant splicing have rarely been reported. Here, we report two unrelated Italian families harboring two different SMAD4 in

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Koeller, Diane R., McKenzie Walker, Busra Unal, et al. "Advancing the Landscape of Clinical Actionability in Von Hippel–Lindau Syndrome: An Evidence-Based Framework from the INT2GRATE Oncology Consortium." Cancers 17, no. 13 (2025): 2173. https://doi.org/10.3390/cancers17132173.

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Background/Objectives: An accurate evaluation of variant actionability is essential in cancer management. In Von Hippel–Lindau Syndrome (VHL), the interpretation of the germline variants is confounded by the presence of non-syndromic component tumors, such as clear cell renal cell carcinoma (ccRCC), hemangioblastoma, pheochromocytoma, and neuroendocrine tumors. These tumors frequently occur sporadically, without any association with VHL syndrome. The presence of these tumors in a patient with a germline VHL variant could lead to inaccurate attribution of these tumors to the germline variant an

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Zavaleta, Elizabeth, Nelly Solis, Maria Isabel Palacios, et al. "Genetic Characterization in High-Risk Individuals from a Low-Resource City of Peru." Cancers 14, no. 22 (2022): 5603. http://dx.doi.org/10.3390/cancers14225603.

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Background: Genetic testing for hereditary cancers is inconsistently applied within the healthcare systems in Latin America. In Peru, the prevalence and spectrum of cancer-predisposing germline variants is thus poorly characterized. Purpose: To determine the spectrum and prevalence of cancer-predisposing germline variants and variants of uncertain significance (VUS) in high-risk individuals located in a Peruvian low-resource setting city. Methods: Individuals presenting clinical criteria for hereditary cancer syndromes or being unaffected with familial history of cancer were included in the st

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Bennett, Mark F., Michael S. Hildebrand, Sayaka Kayumi, et al. "Evidence for a Dual-Pathway, 2-Hit Genetic Model for Focal Cortical Dysplasia and Epilepsy." Neurology Genetics 8, no. 1 (2022): e0652. http://dx.doi.org/10.1212/nxg.0000000000000652.

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Background and ObjectivesThe 2-hit model of genetic disease is well established in cancer, yet has only recently been reported to cause brain malformations associated with epilepsy. Pathogenic germline and somatic variants in genes in the mechanistic target of rapamycin (mTOR) pathway have been implicated in several malformations of cortical development. We investigated the 2-hit model by performing genetic analysis and searching for germline and somatic variants in genes in the mTOR and related pathways.MethodsWe searched for germline and somatic pathogenic variants in 2 brothers with drug-re

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Rana, Huma Q., Diane R. Koeller, McKenzie Walker, et al. "Advancing Precision Oncology in Hereditary Paraganglioma-Pheochromocytoma Syndromes: Integrated Interpretation and Data Sharing of the Germline and Tumor Genomes." Cancers 16, no. 5 (2024): 947. http://dx.doi.org/10.3390/cancers16050947.

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Standard methods of variant assessment in hereditary cancer susceptibility genes are limited by the lack of availability of key supporting evidence. In cancer, information derived from tumors can serve as a useful source in delineating the tumor behavior and the role of germline variants in tumor progression. We have previously demonstrated the value of integrating tumor and germline findings to comprehensively assess germline variants in hereditary cancer syndromes. Building on this work, herein, we present the development and application of the INT2GRATE|HPPGL platform. INT2GRATE (INTegrated

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Pérez-Ibave, Diana Cristina, María Lourdes Garza-Rodríguez, María Fernanda Noriega-Iriondo, et al. "Identification of Germline Variants in Patients with Hereditary Cancer Syndromes in Northeast Mexico." Genes 14, no. 2 (2023): 341. http://dx.doi.org/10.3390/genes14020341.

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Hereditary cancer syndromes (HCS) are genetic diseases with an increased risk of developing cancer. This research describes the implementation of a cancer prevention model, genetic counseling, and germline variants testing in an oncologic center in Mexico. A total of 315 patients received genetic counseling, genetic testing was offered, and 205 individuals were tested for HCS. In 6 years, 131 (63.90%) probands and 74 (36.09%) relatives were tested. Among the probands, we found that 85 (63.9%) had at least one germline variant. We identified founder mutations in BRCA1 and a novel variant in APC

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Reizine, Natalie Marie, Karine Tawagi, Lisa Nuccio, et al. "Alternative model to deliver germline genetic testing to patients with advanced prostate cancer (PCa)." JCO Oncology Practice 19, no. 11_suppl (2023): 123. http://dx.doi.org/10.1200/op.2023.19.11_suppl.123.

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123 Background: Genomic testing is now standard-of-care (SOC) for PCa patients with both therapeutic and hereditable consequences. National guidelines recommend germline testing in all high-risk and advanced PCa patients, regardless of age or family history. Yet, many systemic barriers prevent patients from receiving germline testing promptly, including the burden of appointments, comorbidities, transportation, provider knowledge of genetic testing, and insufficient genetics workforce that limits timely referral to genetic counselors. Methods: We developed a streamlined, alternative genetic ca

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Wheeler, Rebecca, Catherine Terhaar, and Mark Kruzel. "Observed germline BRCA1/2 and TP53 tumor genomic profiling allele frequencies." Journal of Clinical Oncology 42, no. 16_suppl (2024): e22533-e22533. http://dx.doi.org/10.1200/jco.2024.42.16_suppl.e22533.

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e22533 Background: Tumor genomic profiling (TGP) is increasingly used to assist with cancer treatment planning. While these tests are not intended to find germline variants, they are a possible incidental outcome. Currently there are no clear guidelines on when to suspect if a somatic variant identified on TGP may need confirmatory germline genetic testing. Variant allele frequency (VAF) is one tool commonly used to assess if a variant may be germline. While some studies have demonstrated germline VAF ranges on TGP, the data is limited. The purpose of this study was to review VAF ranges of BRC

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Moody, Emily W., Jennie Vagher, Whitney Espinel, David Goldgar, Kelsi J. Hagerty, and Amanda Gammon. "Comparison of Somatic and Germline Variant Interpretation in Hereditary Cancer Genes." JCO Precision Oncology, no. 3 (December 2019): 1–8. http://dx.doi.org/10.1200/po.19.00144.

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PURPOSE To compare the classification of genetic variants reported on tumor genomic profiling (TGP) reports with germline classifications on clinical test results and ClinVar. Results will help to inform germline testing discussions and decisions in patients with tumor variants in genes that are relevant to hereditary cancer risk. PATIENTS AND METHODS This study compared somatic and germline classifications of small nucleotide variants in the following genes: BRCA1, BRCA2, CHEK2, PALB2, ATM, MLH1, MSH2, MSH6, and PMS2. Somatic classifications were taken from reports from a single commercial TG

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Bang, Lisa, Manu Shivakumar, Tullika Garg, and Dokyoon Kim. "Genetic Analysis Reveals Rare Variants in T-Cell Response Gene MR1 Associated with Poor Overall Survival after Urothelial Cancer Diagnosis." Cancers 13, no. 8 (2021): 1864. http://dx.doi.org/10.3390/cancers13081864.

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Urothelial carcinoma of the bladder (UC) is the fifth most common cancer in the United States. Germline variants, especially rare germline variants, may account for a portion of the disparity seen among patients in terms of UC incidence, presentation, and outcomes. The objectives of this study were to identify rare germline variant associations in UC incidence and to determine its association with clinical outcomes. Using exome sequencing data from the DiscovEHR UC cohort (n = 446), a European-ancestry, North American population, the complex influence of germline variants on known clinical phe

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Das, Kingshuk, Amber Carter, Brandie Heald, et al. "Integrated germline and somatic cancer testing provides opportunity to identify cancer risk and resolve variant origins." Journal of Clinical Oncology 40, no. 16_suppl (2022): 10589. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.10589.

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10589 Background: Germline and somatic genetic testing are established tools for the management of cancer patients. Somatic testing is primarily used to inform therapy and germline testing is used to diagnose hereditary cancer predisposition syndromes. While somatic testing can detect germline variants, the interpretation and reporting algorithms are optimized to predict therapeutic efficacy. As a result, germline variants may be missed or only interpreted in context of their potential to act as a therapeutic target. We retrospectively reviewed a series of patients who received both germline a

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Zheng, Hong, Min Gao, Weijiao Gao, et al. "Clinical and genetic characterization of cancer patients with multiple germline variants." Journal of Clinical Oncology 39, no. 15_suppl (2021): e22523-e22523. http://dx.doi.org/10.1200/jco.2021.39.15_suppl.e22523.

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e22523 Background: Hereditary tumors are generally monogenic diseases with autosomal dominant inheritance. However, we noticed that some individuals may harbor ≥2 germline mutations in one or multiple genes, which remains to be explored. Methods: Genetic mutations were reviewed in more than 50,000 cancer patients who underwent hybridization capture based next-generation sequencing (NGS). Germline variants were interpreted following ACMG guideline, and only pathogenic and likely pathogenic variants were included in this study. Results: Multiple germline variants were identified in 42 individual

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Barbosa, Ana, Pedro Pinto, Ana Peixoto, et al. "Gene Panel Tumor Testing in Ovarian Cancer Patients Significantly Increases the Yield of Clinically Actionable Germline Variants beyond BRCA1/BRCA2." Cancers 12, no. 10 (2020): 2834. http://dx.doi.org/10.3390/cancers12102834.

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Since the approval of PARP inhibitors for the treatment of high-grade serous ovarian cancer, in addition to cancer risk assessment, BRCA1 and BRCA2 genetic testing also has therapeutic implications (germline and somatic variants) and should be offered to these patients at diagnosis, irrespective of family history. However, variants in other genes besides BRCA1 and BRCA2 are associated with ovarian cancer predisposition, which would be missed by a genetic testing aimed only at indication for PARP inhibitor treatment. In this study, we aimed to evaluate the yield of clinically actionable germlin

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Guerra, Joana, Carla Pinto, Pedro Pinto, et al. "Frequency of CDH1, CTNNA1 and CTNND1 Germline Variants in Families with Diffuse and Mixed Gastric Cancer." Cancers 15, no. 17 (2023): 4313. http://dx.doi.org/10.3390/cancers15174313.

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The most well-characterized hereditary form of gastric cancer is hereditary diffuse gastric cancer (HDGC), an autosomal dominant syndrome characterized by an increased risk of diffuse gastric and lobular breast cancer. HDGC is predominantly caused by germline pathogenic variants in the CDH1 gene, and more rarely in the CTNNA1 gene. Furthermore, the International Gastric Cancer Linkage Consortium (IGCLC) guidelines do not clarify whether or not mixed gastric cancer (with a diffuse component) should be considered in the HDGC genetic testing criteria. We aimed to evaluate the contribution of CTNN

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Wu, Yanqing, Wenzhe Fan, Miao Xue, et al. "TP53 pathogenic variants with low allele fraction in germline genetic testing." Journal of Clinical Oncology 40, no. 16_suppl (2022): 10600. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.10600.

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10600 Background: Blood or saliva DNA generally considered to be representative of germline genome in genetic cancer risk assessment. However white blood cells from these samples may also include somatic origin DNA due to postzygotic variation or, most commonly, clonal hematopoiesis (CH). Low variant allele fraction (VAF) found in germline genetic testing suggest the possibility of somatic variant and may lead to misinterpretation of genetic risk. TP53, of which germline pathogenic variants are associated with Li-Fraumeni syndrome (LFS), is frequently mutated in CH. This analysis investigated

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Pasternak, Amy L., Kristen M. Ward, Jasmine A. Luzum, Vicki L. Ellingrod, and Daniel L. Hertz. "Germline genetic variants with implications for disease risk and therapeutic outcomes." Physiological Genomics 49, no. 10 (2017): 567–81. http://dx.doi.org/10.1152/physiolgenomics.00035.2017.

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Genetic testing has multiple clinical applications including disease risk assessment, diagnosis, and pharmacogenomics. Pharmacogenomics can be utilized to predict whether a pharmacologic therapy will be effective or to identify patients at risk for treatment-related toxicity. Although genetic tests are typically ordered for a distinct clinical purpose, the genetic variants that are found may have additional implications for either disease or pharmacology. This review will address multiple examples of germline genetic variants that are informative for both disease and pharmacogenomics. The disc

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Wu, Wendy Yi-Ying, Gunnar Johansson, Carl Wibom, et al. "The Genetic Architecture of Gliomagenesis–Genetic Risk Variants Linked to Specific Molecular Subtypes." Cancers 11, no. 12 (2019): 2001. http://dx.doi.org/10.3390/cancers11122001.

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Genome-wide association studies have identified 25 germline genetic loci that increase the risk of glioma. The somatic tumor molecular alterations, including IDH-mutation status and 1p/19q co-deletion, have been included into the WHO 2016 classification system for glioma. To investigate how the germline genetic risk variants correlate with the somatic molecular subtypes put forward by WHO, we performed a meta-analysis that combined findings from 330 Swedish cases and 876 controls with two other recent studies. In total, 5,103 cases and 10,915 controls were included. Three categories of associa

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DiNardo, Courtney D., Larissa A. Korde, and Matthew B. Yurgelun. "A Case-Based Approach to Understanding Complex Genetic Information in an Evolving Landscape." American Society of Clinical Oncology Educational Book, no. 41 (June 2021): e328-e338. http://dx.doi.org/10.1200/edbk_321041.

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The rapid integration of highly sensitive next-generation sequencing technologies into clinical oncology care has led to unparalleled progress, and yet these technological advances have also made genetic information considerably more complex. For instance, accurate interpretation of genetic testing for germline/inherited cancer predisposition syndromes and somatic/acquired pathogenic variants now requires a more nuanced understanding of the presence and incidence of clonal hematopoiesis and circulating tumor cells, with careful evaluation of pathogenic variants occurring at low variant allele

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Ehsan, Hamid, James Thomas Symanowski, Aly Athens, et al. "Utilization of germline testing in patients with early-onset pancreatic cancer (EOPC)." Journal of Clinical Oncology 41, no. 16_suppl (2023): e16300-e16300. http://dx.doi.org/10.1200/jco.2023.41.16_suppl.e16300.

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e16300 Background: EOPC is associated with significant life years lost. Approximately 5%-10% of pancreatic adenocarcinoma (PAC) have an underlying genetic predisposition and national guidelines recommend testing in all patients with PAC. Certain germline mutations such as BRCA2 and PALB2 predict response to specific treatments including platinum and targeted therapies. It is currently unknown to what extent patients with EOPC pursue recommended germline testing. We examined the utilization of germline testing in patients with EOPC who were referred to genetics. Methods: A retrospective review

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Kohlmann, Wendy, David Nix, Aaron Atkinson, et al. "Inherited germline variants in urothelial cancer: A multicenter whole-exome sequencing analysis." Journal of Clinical Oncology 40, no. 6_suppl (2022): 451. http://dx.doi.org/10.1200/jco.2022.40.6_suppl.451.

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451 Background: Outside of Lynch syndrome, few genetic factors have been associated with urothelial cancer (UC). This project seeks to describe the frequency of germline variants in a multi-center UC cohort. Methods: Patients diagnosed with UC from 1980 to 2019 and consented to the Total Cancer Care protocol by members of the Oncology Research Information Exchange Network (ORIEN) were included in the study. The ORIEN program includes a convenience sample of cases with both germline and tumor samples available, though this analysis was germline only. Whole exome sequencing data were analyzed us

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Goebel, Emily A., Jennifer Kerkhof, Oleksandra Dzyubak, C. Meg McLachlin, Jacob McGee, and Bekim Sadikovic. "Examining the Diagnostic Yield of Tumour Testing and Qualifying Germline Concordance for Hereditary Cancer Variants in Patients with High-Grade Serous Carcinoma." Genes 13, no. 8 (2022): 1398. http://dx.doi.org/10.3390/genes13081398.

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Despite advances in treatment, prognosis for most patients with high-grade serous carcinoma (HGSC) remains poor. Genomic alterations in the homologous recombination (HR) pathway are used for cancer risk assessment and render tumours sensitive to platinum-based chemotherapy and poly (ADP-ribose) polymerase inhibitors (PARPi), which can be associated with more favourable outcomes. In addition to patients with tumours containing BRCA1 or BRCA2 pathologic variants, there is emerging evidence that patients with tumours harbouring pathologic variants in other HR genes may also benefit from PARPi the

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Moriyama, Takaya, Monika Metzger, Gang Wu, et al. "Germline Genetic Variation in ETV6 and Predisposition to Childhood Acute Lymphoblastic Leukemia." Blood 126, no. 23 (2015): 695. http://dx.doi.org/10.1182/blood.v126.23.695.695.

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Abstract Acute lymphoblastic leukemia (ALL) is the most common cancer in children, and the etiology of this aggressive cancer is not fully understood. Common germline polymorphisms in lymphoid development genes and tumor suppressor genes have been associated with ALL susceptibility, although most have modest effects. Only a small fraction of ALL cases are thought to be related to congenital genetic disorders and consequently hereditary predisposition is rarely considered in clinical practice. However, a growing number of rare germline genetic mutations have been discovered in familial ALL (e.g

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Jajosky, Audrey N., Anna L. Mitchell, Mahmut Akgul, et al. "Identification of a Cancer-Predisposing Germline POT1 p.Ile49Metfs*7 Variant by Targeted Sequencing of a Splenic Marginal Zone Lymphoma." Genes 13, no. 4 (2022): 591. http://dx.doi.org/10.3390/genes13040591.

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Germline disruptive variants in Protection of Telomeres 1 (POT1) predispose to a wide variety of cancers, including melanoma, chronic lymphocytic leukemia (CLL), Hodgkin lymphoma, myeloproliferative neoplasms, and glioma. We report the first case of splenic marginal zone lymphoma (SMZL) arising in a patient with a germline POT1 variant: a 65-year-old male with an extensive history of cancer, including melanoma and papillary thyroid carcinoma, who presented with circulating atypical lymphocytosis. Bone marrow biopsy revealed 20% involvement by a CD5−CD10− B-cell lymphoma that was difficult to c

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Sylvester, Dianne E., Yuyan Chen, Robyn V. Jamieson, Luciano Dalla-Pozza, and Jennifer A. Byrne. "Investigation of clinically relevant germline variants detected by next-generation sequencing in patients with childhood cancer: a review of the literature." Journal of Medical Genetics 55, no. 12 (2018): 785–93. http://dx.doi.org/10.1136/jmedgenet-2018-105488.

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Genetic predisposition is an important underlying cause of childhood cancer, although the proportion of patients with childhood cancer carrying predisposing pathogenic germline variants is uncertain. This review considers the pathogenic or likely pathogenic germline variants reported by six studies that used next-generation sequencing to investigate genetic predisposition in selected cohorts of patients with childhood cancer and used incompletely overlapping gene sets for analysis and interpretation. These six studies reported that 8.5%–35.5% of patients with childhood cancer carried clinicall

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Carvalho, Joana, Patricia Oliveira, Janine Senz, et al. "Redefinition of familial intestinal gastric cancer: clinical and genetic perspectives." Journal of Medical Genetics 58, no. 1 (2020): 1–11. http://dx.doi.org/10.1136/jmedgenet-2019-106346.

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BackgroundFamilial intestinal gastric cancer (FIGC) remains genetically unexplained and without testing/clinical criteria. Herein, we characterised the age of onset and disease spectrum of 50 FIGC families and searched for genetic causes potentially underlying a monogenic or an oligogenic/polygenic inheritance pattern.MethodsNormal and tumour DNA from 50 FIGC probands were sequenced using Illumina custom panels on MiSeq, and their respective germline and somatic landscapes were compared with corresponding landscapes from sporadic intestinal gastric cancer (SIGC) and hereditary diffuse gastric

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Hosoya, Noriko, and Kiyoshi Miyagawa. "Implications of the germline variants of DNA damage response genes detected by cancer precision medicine for radiological risk communication and cancer therapy decisions." Journal of Radiation Research 62, Supplement_1 (2021): i44—i52. http://dx.doi.org/10.1093/jrr/rrab009.

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ABSTRACT Large-scale cancer-associated gene testing is now being rapidly incorporated into clinical settings, and is leading to incidental identification of the germline variants present in cancer patients. Because many cancer susceptibility genes are related to DNA damage response and repair, the variants may reflect not only the susceptibility to cancer but also the genetically defined radiation sensitivity of the patients and their relatives. When the presence of a certain germline variant increases the risk for developing radiation toxicity or radiation-induced secondary cancers, it will g

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Frone, Megan N., Douglas R. Stewart, Sharon A. Savage, and Payal P. Khincha. "Quantification of Discordant Variant Interpretations in a Large Family-Based Study of Li-Fraumeni Syndrome." JCO Precision Oncology, no. 5 (November 2021): 1727–37. http://dx.doi.org/10.1200/po.21.00320.

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PURPOSE The use of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology guidelines has improved germline variant classification concordance, but discrepancies persist, sometimes directly affecting medical management. We evaluated variant discordance between and within families with germline TP53 variants in the National Cancer Institute's Li-Fraumeni syndrome longitudinal cohort study. MATERIALS AND METHODS Germline TP53 genetic testing results were obtained from 421 individuals in 140 families. A discordant test result was defined as a report of pa

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DeLeonardis, Kim, Lauren Hogan, Stephen A. Cannistra, Deepa Rangachari, and Nadine Tung. "When Should Tumor Genomic Profiling Prompt Consideration of Germline Testing?" Journal of Oncology Practice 15, no. 9 (2019): 465–73. http://dx.doi.org/10.1200/jop.19.00201.

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Somatic genomic testing is rapidly becoming an integral part of care for patients with metastatic cancer. Extrapolation of these results beyond personalized cancer therapy is a skill being demanded of practicing oncologists without prior specialty in genetics. Up to 12% of tumor genomic profiling reports will reveal a germline pathogenic variant. Recognition of these germline variants is essential not only for optimal care of the patient with cancer but also to initiate cascade genetic testing in at-risk family members who also may carry the familial mutation. This article provides a concise a

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Garza-Rodríguez, María Lourdes, Víctor Treviño, Antonio Alí Pérez-Maya, et al. "Identification of a Novel Pathogenic Rearrangement Variant of the APC Gene Associated with a Variable Spectrum of Familial Cancer." Diagnostics 11, no. 3 (2021): 411. http://dx.doi.org/10.3390/diagnostics11030411.

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Familial adenomatous polyposis (FAP) is an autosomal-dominant condition characterized by the presence of multiple colorectal adenomas, caused by germline variants in the adenomatous polyposis coli (APC) gene. More than 300 germline variants have been characterized. The detection of novel variants is important to understand the mechanisms of pathophysiology. We identified a novel pathogenic germline variant using next-generation sequencing (NGS) in a proband patient. The variant is a complex rearrangement (c.422+1123_532-577 del ins 423-1933_423-1687 inv) that generates a complete deletion of e

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Whitworth, Pat W., Peter D. Beitsch, Rakesh Patel, et al. "Clinical Utility of Universal Germline Genetic Testing for Patients With Breast Cancer." JAMA Network Open 5, no. 9 (2022): e2232787. http://dx.doi.org/10.1001/jamanetworkopen.2022.32787.

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ImportanceNational Comprehensive Cancer Network guidelines currently recommend germline testing for high-risk genes in selected patients with breast cancer. The clinical utility of recommending testing all patients with breast cancer with multigene panels is currently under consideration.ObjectiveTo examine the implications of universal testing of patients with breast cancer with respect to clinical decision-making.Design, Setting, and ParticipantsPatients from a previously reported cohort were assessed as in-criteria or out-of-criteria according to the 2017 guidelines and underwent testing wi

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Retnomawarti, Rizka, Sonar Soni Panigoro, and Rafika Indah Paramita. "The Bioinformatics Application in Detecting Germline and Somatic Variants towards Breast Cancer using Next Generation Sequencing." Journal of Applied Science, Engineering, Technology, and Education 5, no. 1 (2023): 25–34. http://dx.doi.org/10.35877/454ri.asci1608.

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Breast cancer is the type of cancer with the most and the highest cases causing mortality in Indonesia, so an effective treatment is required to reduce the incidence and mortality rate due to cancer breasts. Most breast cancer patients are diagnosed at an advanced stage so the treatment used are limited and the risk of death becomes higher. Along with the development of human genome sequencing technology, the genetic examination of breast cancer is considered as an examination that can be used for early prevention and treatment management personally. Based on the target variants detected, the

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Skopelitou, Diamanto, Beiping Miao, Aayushi Srivastava, et al. "Whole Exome Sequencing Identifies APCDD1 and HDAC5 Genes as Potentially Cancer Predisposing in Familial Colorectal Cancer." International Journal of Molecular Sciences 22, no. 4 (2021): 1837. http://dx.doi.org/10.3390/ijms22041837.

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Germline mutations in predisposition genes account for only 20% of all familial colorectal cancers (CRC) and the remaining genetic burden may be due to rare high- to moderate-penetrance germline variants that are not explored. With the aim of identifying such potential cancer-predisposing variants, we performed whole exome sequencing on three CRC cases and three unaffected members of a Polish family and identified two novel heterozygous variants: a coding variant in APC downregulated 1 gene (APCDD1, p.R299H) and a non-coding variant in the 5′ untranslated region (UTR) of histone deacetylase 5

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Potnis, Kunal, Quinn Ostrom, and Elizabeth Claus. "EPID-06. ASSOCIATIONS BETWEEN GERMLINE GENETIC VARIANTS AND OVERALL SURVIVAL IN PATIENTS WITH GLIOMA." Neuro-Oncology 23, Supplement_6 (2021): vi86. http://dx.doi.org/10.1093/neuonc/noab196.339.

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Abstract BACKGROUND In addition to somatic genetic variation in tumors, germline genetic variation can better define cancer susceptibility risk, guide therapy, and predict survival. Most prior research into associations between germline genetic variants and survival outcomes in patients with glioma has been limited by small sample sizes and to high-grade glioma only. This study is the first to use data from Brigham and Women’s Hospital (BWH) and to include both low-grade and high-grade glioma cases to explore associations between germline genetic variants and overall survival. METHODS This stu

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Abu-Hijlih, Ramiz, Baha Sharaf, Samer Salah, et al. "Germline Genetic Mutations in Adult Patients with Sarcoma: Insight into the Middle East Genetic Landscape." Cancers 16, no. 9 (2024): 1668. http://dx.doi.org/10.3390/cancers16091668.

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Data on germline mutations in soft tissue and bone sarcomas are scarce. We sought to identify the prevalence of germline mutations in adult sarcoma patients treated at a tertiary cancer center. Newly diagnosed patients were offered germline genetic testing via an 84-gene panel. The prevalence of pathogenic germline variants (PGVs) and their association with disease-, and patient- related factors are reported. A total of 87 patients were enrolled, the median age was 48 (19–78) years, and 47 (54%) were females. Gastrointestinal stromal tumors (n = 12, 13.8%), liposarcoma (n = 10, 11.5%), and Ewi

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Chavarri Guerra, Yanin, Sharon Sand, Sandra Brown, et al. "Germline cancer susceptibility mutations in older women with breast cancer (BC)." Journal of Clinical Oncology 35, no. 15_suppl (2017): e13030-e13030. http://dx.doi.org/10.1200/jco.2017.35.15_suppl.e13030.

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e13030 Background: Older women with BC are less likely to undergo genetic cancer risk assessment since a hallmark of hereditary BC is younger age at onset. Hence there are limited data regarding genetic risk assessment findings in older women with BC. We analyzed the clinical characteristics and germline variant profiles of women with history of BC referred for genetic counseling at age ≥ 65 years, enrolled in the Clinical Cancer Genomics Community Research Network registry. Methods: Women age ≥ 65 with a history of BC (invasive or ductal carcinoma in situ) who underwent genetic testing from 1

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Feurstein, Simone K., Amy M. Trottier, Noel Estrada-Merly, et al. "Deleterious Germline Variants Are Present in Patients with Myelodysplastic Syndrome of All Ages Treated with Related Allogeneic Stem Cell Transplantation." Blood 138, Supplement 1 (2021): 320. http://dx.doi.org/10.1182/blood-2021-148866.

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Abstract Inherited myeloid malignancies are included as a provisional category in the current World Health Organization classification and within clinical testing guidelines of the National Comprehensive Cancer Network for myelodysplastic syndrome (MDS) and the European LeukemiaNet. The frequency of deleterious germline variants in MDS patients diagnosed at or younger than 40 years old ranges from 15-20%. To determine the frequency of germline predisposition in MDS patients of all ages, we accessed peripheral blood samples collected by the Center for International Blood and Marrow Transplant R

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McQuaid, Shelly W., Rebecca Kaufman, Ryan J. Corbett, et al. "METB-09. GERMLINE PATHOGENIC VARIANTS IN 838 PEDIATRIC BRAIN TUMOR PATIENTS." Neuro-Oncology 25, Supplement_1 (2023): i32. http://dx.doi.org/10.1093/neuonc/noad073.126.

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Abstract The genetic contribution of rare pathogenic germline variation in cancer patients without a family history remains unclear. We sought to characterize the prevalence, spectrum, and clinical significance of pathogenic germline variation in cancer predisposition genes (CPGs) in pediatric brain tumor patients. Paired tumor and normal whole genome or exome sequencing was performed for 838 patients in the Pediatric Brain Tumor Atlas (PBTA). Rare variants in 196 CPGs were annotated as pathogenic (P) or likely pathogenic (LP) in an automated manner consistent with American College of Medical

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Esplin, Edward, Shan Yang, Scott T. Michalski, et al. "Determining the clinical value of germline genetic testing coupled with tumor mutation profiling." Journal of Clinical Oncology 35, no. 15_suppl (2017): 1577. http://dx.doi.org/10.1200/jco.2017.35.15_suppl.1577.

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1577 Background: Somatic mutation analysis by next-generation sequencing (NGS) is an expanding clinical assessment offered to cancer patients. Studies report that 4–12% of patients have a positive tumor mutation profiling (TMP) result in a known cancer predisposition gene also identified in their germline, which has potential implications for the patient’s acute treatment, ongoing surveillance, and the screening of family members. We report a series of patients with TMP coupled with germline genetic testing and include yield of pathogenic germline mutations, discordance between germline and TM

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Moriyama, Takaya, Mary V. Relling, and Jun J. Yang. "Inherited genetic variation in childhood acute lymphoblastic leukemia." Blood 125, no. 26 (2015): 3988–95. http://dx.doi.org/10.1182/blood-2014-12-580001.

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Abstract Although somatically acquired genomic alterations have long been recognized as the hallmarks of acute lymphoblastic leukemia (ALL), the last decade has shown that inherited genetic variations (germline) are important determinants of interpatient variability in ALL susceptibility, drug response, and toxicities of ALL therapy. In particular, unbiased genome-wide association studies have identified germline variants strongly associated with the predisposition to ALL in children, providing novel insight into the mechanisms of leukemogenesis and evidence for complex interactions between in

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Zhang, Yinjie, Xicheng Wang, Changbin Zhu, et al. "A multi-institutional investigation assessing prevalence of germline genetic alterations in Chinese patients with gastric carcinoma." Journal of Clinical Oncology 37, no. 15_suppl (2019): e13020-e13020. http://dx.doi.org/10.1200/jco.2019.37.15_suppl.e13020.

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e13020 Background: Gastric carcinoma is one of the most common malignancies in east asian. Previous studies demonstrated around 10% of patients with gastric cancer were found to have pathogenic germline variants. While, predisposition genes of gastric cancer in Chinese patients are still largely unknown. Thus, we aim to delineate prevalence of deleterious germline mutations in Chinese gastric patients with hereditary high-risk familial cancer history. We also aim to analyze clinical relevance of deleterious germline mutations. Methods: Forty index cases were recruited from 7 institutions in Ch

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