Identification of germline cancer predisposition variants during clinical ctDNA testing.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e15555-e15555
Author(s):  
Leigh Anne Anne Stout ◽  
Nawal Kassem ◽  
Cynthia Hunter ◽  
Santosh Philips ◽  
Milan Radovich ◽  
...  
Keyword(s):  
Allele Frequency ◽  
Metastatic Cancer ◽  
Circulating Tumor Dna ◽  
Cancer Predisposition ◽  
Germline Variants ◽  
Predisposition Genes ◽  
Invasive Method ◽  
Ctdna Analysis ◽  
High Level ◽  
Germline Testing

e15555 Background: Next-generation sequencing (NGS) of circulating tumor DNA (ctDNA) is a non-invasive method to guide therapy selection for cancer patients. Identification of inherited germline cancer predisposition mutations that have significant implications for at-risk relatives may be missed during routine ctDNA testing. Allele frequency has the potential to enhance the likelihood that a mutation is germline; and is often reported in many NGS tests from ctDNA. Here, we report on the fidelity of allele frequency in ctDNA as a predictor for pathogenic germline variant carriage. Methods: ctDNA sequencing of patients with metastatic cancer from the Indiana University Health Precision Genomics Program was performed using the FoundationOne Liquid assay. All variants detected by the ctDNA assay report were considered. All patients also had germline testing information and pathogenicity of germline variants were determined using ClinVar. Germline variants with conflicting interpretations were manually reviewed to determine pathogenicity. Comparisons between ctDNA results with known germline status were performed. Results: Of 91 previously identified germline cancer predisposition variants, 36 (40%) were also identified by ctDNA analysis. All germline variants that were tested for in the ctDNA assay (n = 36, 100%) were identified. When detected, the allele frequencies of detected germline variants in the ctDNA ranged from 39-87.6% with an average of 52.1%. Conversely, 111 of 160 (69%) variants identified by ctDNA analysis with allele frequency between 40-60% in a cancer predisposition gene were found to be germline in origin (regardless of pathogenicity). Variants in the BRCA2, BRCA1, and CDH1 genes were most likely to be germline in origin (26/27 [96%], 20/22 [91%], 13/15 [87%], respectively). Variants in the TP53 and APC genes were least likely to be germline in origin (9/36 [25%] and 1/6 [17%], respectively). There was an 85% (95/111) concordance in actionability between the somatic testing lab and ClinVar germline classifications. Of the 16 discordant variants, 100% were determined to be actionable by the somatic testing lab but not actionable in ClinVar. Conclusions: ctDNA allele frequency can alter the likelihood that a variant is germline. Importantly, however, this testing is far from comprehensive and should not be used as a replacement for germline testing. Variants with allele frequency between 40-60% in cancer predisposition genes should induce a high level of suspicion for germline status.

scholarly journals Identification of germline cancer predisposition variants during clinical ctDNA testing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Leigh Anne Stout ◽  
Nawal Kassem ◽  
Cynthia Hunter ◽  
Santosh Philips ◽  
Milan Radovich ◽  
...  
Keyword(s):  
Circulating Tumor Dna ◽  
Variant Allele Frequency ◽  
Germline Variants ◽  
Non Invasive ◽  
Invasive Method ◽  
Selection For ◽  
Ctdna Analysis ◽  
Tumor Dna ◽  
Generation Sequencing ◽  
Germline Testing

AbstractNext-generation sequencing of circulating tumor DNA (ctDNA) is a non-invasive method to guide therapy selection for cancer patients. ctDNA variant allele frequency (VAF) is commonly reported and may aid in discerning whether a variant is germline or somatic. We report on the fidelity of VAF in ctDNA as a predictor for germline variant carriage. Two patient cohorts were studied. Cohort 1 included patients with known germline variants. Cohort 2 included patients with any variant detected by the ctDNA assay with VAF of 40–60%. In cohort 1, 36 of 91 (40%) known germline variants were identified through ctDNA analysis with a VAF of 39–87.6%. In cohort 2, 111 of 160 (69%) variants identified by ctDNA analysis with a VAF between 40 and 60% were found to be germline. Therefore, variants with a VAF between 40 and 60% should induce suspicion for germline status but should not be used as a replacement for germline testing.

scholarly journals Identification of Germline Cancer Predisposition Variants During Clinical Ctdna Testing

2021 ◽  
Author(s):  
Leigh Anne Stout ◽  
Nawal Kassem ◽  
Cynthia Hunter ◽  
Santosh Philips ◽  
Milan Radovich ◽  
...  
Keyword(s):  
Circulating Tumor Dna ◽  
Variant Allele Frequency ◽  
Germline Variants ◽  
Non Invasive ◽  
Invasive Method ◽  
Selection For ◽  
Ctdna Analysis ◽  
Next Generation Sequencing Ngs ◽  
Tumor Dna ◽  
Generation Sequencing

Abstract Next-generation sequencing (NGS) of circulating tumor DNA (ctDNA) is a non-invasive method to guide therapy selection for cancer patients. ctDNA variant allele frequency (VAF) is commonly reported and may aid in discerning whether a variant is germline or somatic. We report on the fidelity of VAF in ctDNA as a predictor for germline variant carriage. Two patient cohorts were studied. Cohort 1 included patients with known germline variants. Cohort 2 included patients with any variant detected by the ctDNA assay with VAF of 40–60%. In cohort 1, 36 of 91 (40%) known germline variants were identified through ctDNA analysis with a VAF of 39-87.6%. In cohort 2, 111 of 160 (69%) variants identified by ctDNA analysis with a VAF between 40–60% were found to be germline. Therefore, variants with a VAF between 40–60% should induce suspicion for germline status but should not be used as a replacement for germline testing.

Primer on Hereditary Cancer Predisposition Genes Included Within Somatic Next-Generation Sequencing Panels

2019 ◽  
pp. 1-11
Author(s):  
Zade Akras ◽  
Brandon Bungo ◽  
Brandie H. Leach ◽  
Jessica Marquard ◽  
Manmeet Ahluwalia ◽  
...  
Keyword(s):  
Hereditary Cancer ◽  
Cancer Susceptibility ◽  
Cancer Predisposition ◽  
Comprehensive Overview ◽  
Germline Variants ◽  
Cancer Susceptibility Genes ◽  
Germline Genes ◽  
Number Of Genes ◽  
Predisposition Genes ◽  
Hereditary Cancer Predisposition

PURPOSE It has been estimated that 5% to 10% of cancers are due to hereditary causes. Recent data sets indicate that the incidence of hereditary cancer may be as high as 17.5% in patients with cancer, and a notable subset is missed if screening is solely by family history and current syndrome-based testing guidelines. Identification of germline variants has implications for both patients and their families. There is currently no comprehensive overview of cancer susceptibility genes or inclusion of these genes in commercially available somatic testing. We aimed to summarize genes linked to hereditary cancer and the somatic and germline panels that include such genes. METHODS Germline predisposition genes were chosen if commercially available for testing. Penetrance was defined as low, moderate, or high according to whether the gene conferred a 0% to 20%, 20% to 50%, or 50% to 100% lifetime risk of developing the cancer or, when percentages were not available, was estimated on the basis of existing literature descriptions. RESULTS We identified a total of 89 genes linked to hereditary cancer predisposition, and we summarized these genes alphabetically and by organ system. We considered four germline and six somatic commercially available panel tests and quantified the coverage of germline genes across them. Comparison between the number of genes that had germline importance and the number of genes included in somatic testing showed that many but not all germline genes are tested by frequently used somatic panels. CONCLUSION The inclusion of cancer-predisposing genes in somatic variant testing panels makes incidental germline findings likely. Although somatic testing can be used to screen for germline variants, this strategy is inadequate for comprehensive screening. Access to genetic counseling is essential for interpretation of germline implications of somatic testing and implementation of appropriate screening and follow-up.

scholarly journals Understanding Inherited Risk in Unselected Newly Diagnosed Patients With Endometrial Cancer

2019 ◽  
pp. 1-15
Author(s):  
Karen A. Cadoo ◽  
Diana L. Mandelker ◽  
Semanti Mukherjee ◽  
Carolyn Stewart ◽  
Deborah DeLair ◽  
...  
Keyword(s):  
Endometrial Cancer ◽  
Next Generation Sequencing ◽  
Lynch Syndrome ◽  
Microsatellite Instability ◽  
Mismatch Repair ◽  
Cancer Predisposition ◽  
Next Generation ◽  
Germline Variants ◽  
Predisposition Genes ◽  
Generation Sequencing

PURPOSE Mutations in DNA mismatch repair genes and PTEN, diagnostic of Lynch and Cowden syndromes, respectively, represent the only established inherited predisposition genes in endometrial cancer to date. The prevalence of other cancer predisposition genes remains unclear. We determined the prevalence of pathogenic germline variants in unselected patients with endometrial cancer scheduled for surgical consultation. PATIENTS AND METHODS Patients prospectively consented (April 2016 to May 2017) to an institutional review board–approved protocol of tumor-normal sequencing via a custom next-generation sequencing panel—the Memorial Sloan Kettering–Integrated Mutation Profiling of Actionable Cancer Targets—that yielded germline results for more than 75 cancer predisposition genes. Tumors were assessed for microsatellite instability. Per institutional standards, all tumors underwent Lynch syndrome screening via immunohistochemistry (IHC) for mismatch repair proteins. RESULTS Of 156 patients who consented to germline genetic testing, 118 (76%) had stage I disease. In 104 patients (67%), tumors were endometrioid, and 60 (58%) of those tumors were grade 1. Twenty-four pathogenic germline variants were identified in 22 patients (14%): seven (4.5%) had highly penetrant cancer syndromes and 15 (9.6%) had variants in low-penetrance, moderate-penetrance, or recessive genes. Of these, five (21%) were in Lynch syndrome genes (two MSH6, two PMS2, and one MLH1). All five tumors had concordant IHC staining; two (40%) were definitively microsatellite instability–high by next-generation sequencing. One patient had a known BRCA1 mutation, and one had an SMARCA4 deletion. The remaining 17 variants (71%) were incremental findings in low- and moderate-penetrance variants or genes associated with recessive disease. CONCLUSION In unselected patients with predominantly low-risk, early-stage endometrial cancer, germline multigene panel testing identified cancer predisposition gene variants in 14%. This finding may have implications for future cancer screening and risk-reduction recommendations. Universal IHC screening for Lynch syndrome successfully identifies the majority (71%) of high-penetrance germline mutations.

scholarly journals Identification of Incidental Germline Mutations in Patients With Advanced Solid Tumors Who Underwent Cell-Free Circulating Tumor DNA Sequencing

2018 ◽  
Vol 36 (35) ◽  
pp. 3459-3465 ◽  
Author(s):  
Thomas P. Slavin ◽  
Kimberly C. Banks ◽  
Darya Chudova ◽  
Geoffrey R. Oxnard ◽  
Justin I. Odegaard ◽  
...  
Keyword(s):  
Hereditary Cancer ◽  
Germline Mutations ◽  
Circulating Tumor Dna ◽  
Cancer Predisposition ◽  
Cancer Genetic Counseling ◽  
Predisposition Genes ◽  
Average Patient ◽  
Cancer Types ◽  
Tumor Dna ◽  
Hereditary Cancer Predisposition

Purpose To determine the potential for detection of incidental germline cancer predisposition mutations through cell-free DNA (cfDNA) analyses in patients who underwent solid tumor somatic mutation evaluation. Patients and Methods Data were evaluated from 10,888 unselected patients with advanced (stage III/IV) cancer who underwent Guardant360 testing between November 2015 and December 2016. The main outcome was prevalence of putative germline mutations identified among 16 actionable hereditary cancer predisposition genes. Results More than 50 cancer types were studied, including lung (41%), breast (19%), colorectal (8%), prostate (6%), pancreatic (3%), and ovarian (2%). Average patient age was 63.5 years (range, 18 to 95 years); 43% were male. One hundred and fifty-six individuals (1.4%) had suspected hereditary cancer mutations in 11 genes. Putative germline mutations were more frequent in individuals younger than 50 years versus those 50 years and older (3.0% v 1.2%, respectively; P < .001). Highest yields of putative germline findings were in patients with ovarian (8.13%), prostate (3.46%), pancreatic (3.34%), and breast (2.2%) cancer. Putative germline mutation identification was consistent among 12 individuals with multiple samples. Patients with circulating tumor DNA copy number variation and/or reversion mutations suggestive of functional loss of the wild-type allele in the tumor DNA also are described. Conclusion Detection of putative germline mutations from cfDNA is feasible across multiple genes and cancer types without prior mutation knowledge. Many mutations were found in cancers without clear guidelines for hereditary cancer genetic counseling/testing. Given the clinical significance of identifying hereditary cancer predisposition for patients and their families as well as targetable germline alterations such as in BRCA1 or BRCA2, research on the best way to validate and return potential germline results from cfDNA analysis to clinicians and patients is needed.

scholarly journals Germline Variants Associated with Cancer Predisposition and Bone Marrow Failure Are Common in KMT2A-r Infant Acute Lymphoblastic Leukemia Patients

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 41-41
Author(s):  
Sarah Mc Dermott ◽  
Midhat S. Farooqi ◽  
Azhar Saeed ◽  
Byunggil Yoo ◽  
Emily Farrow ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Acute Lymphoblastic Leukemia ◽  
Board Of Directors ◽  
Bone Marrow Failure ◽  
Lymphoblastic Leukemia ◽  
Cancer Predisposition ◽  
Advisory Committees ◽  
Germline Variants ◽  
Predisposition Genes ◽  
Infant Acute Lymphoblastic Leukemia

Introduction: Infant acute lymphoblastic leukemia (ALL), is a particularly aggressive subtype of leukemia with an early onset and unfavorable clinical outcome. Most (~70%) cases of infant ALL involve chromosomal rearrangement of KMT2A (KMT2A-r) on chromosome 11q23, the strongest independent predictor of a poor prognosis. To date, genomics studies have consistently demonstrated KMT2A-r infant ALL to have a strikingly silent landscape of DNA mutations, aside from the KMT2A-r itself. Germline mutations in cancer predisposition genes are found in 8.6% of pediatric malignancies and 4.4% of pediatric leukemias, compared to 1.1% in persons in the 1000 Genomes Project (Zhang J et al., N Engl J Med 2015). We hypothesized that germline variants may contribute to the development of KMT2A-r ALL in infants. We examined the germline variants in remission blood samples from a large cohort of infants with KMT2A-r ALL who were enrolled in Children's Oncology Group (COG) trial AALL15P1. Methods: We performed whole genome sequencing (WGS) and whole exome sequencing (WES) on DNA isolated from peripheral blood from 36 KMT2A-r cases at time of remission. Sequencing was performed using an Illumina Hiseq 4000 or 2500 to a minimum depth of 90Gb (WGS) and 15Gb (WES). Alignment and variant calling were performed using the Dragon Bio-IT platform (v 3.2.8, Illumina). Blueprint Genetics clinical panels and the medical literature (Xa M et al., Nature 2018) were used to comprise a list of 346 genes associated with cancer predisposition and bone marrow failure syndromes. From this gene pool, variants were selected for analysis based on a variant allele frequency of ~50% and minor allele frequency &lt;0.1% in control population databases (gnomAD). Variants were analyzed for pathogenicity per the 2015 ACMG/AMP interpretation guidelines for sequence variants. Results: Of 351 variants initially identified, we found 3 likely pathogenic (LP) and 6 pathogenic(P) non-synonymous germline variants (for a total of 9 LP/P variants) and 144 variants of unknown significance (VUS). In total, 19.4% (n=7) of patient samples displayed at least one LP/P variant. Two patient samples contained 2 variants each. Variants classified as VUS, LP, or P were further characterized by possible causative pathway: 37.9% (n=58) of variants were in genes associated with bone marrow failure (BMF), 17.6% (n=27) in driver genes, 13.1% (n=20) in genes associated with inherited leukemias, 11.1% (n=17) in tumor suppressor genes, 7.8% (n=12) in tyrosine kinase genes, and 29.4% (n=45) in other predisposition genes . Many variants were present in more than one pathway and are represented as such. Table 1 demonstrates the genetic characteristics of the 9 P/LP variants found in our cohort. ERCC2 was the only gene with multiple LP/P variants across samples, accounting for 2 (1 LP, 1 P) of the 9 deleterious variants identified (22%). Conclusion: We identified germline variants in cancer predisposition genes in 19.4% of this cohort of infant ALL patients, a higher mutation rate than has previously been reported. Among pathways evaluated, variants in genes associated with bone marrow failure predisposition were the most frequent. Interestingly, variants in ERCC2, which encodes a protein involved with repair of damaged DNA, were recurrent among infants with KMT2A-r ALL. Future directions include comparison to germline variants in cancer predisposition genes in other infant and non-infant ALL cohorts. Disclosures Brown: Novartis: Membership on an entity's Board of Directors or advisory committees; Jazz: Membership on an entity's Board of Directors or advisory committees; Servier: Membership on an entity's Board of Directors or advisory committees; Janssen: Membership on an entity's Board of Directors or advisory committees. Guest:Syndax Pharmaceuticals: Consultancy.

scholarly journals Substantial Batch Effects in TCGA Exome Sequences Undermine Pan-Cancer Analysis of Germline Variants

2018 ◽  
Author(s):  
Roni Rasnic ◽  
Nadav Brandes ◽  
Or Zuk ◽  
Michal Linial
Keyword(s):  
Cancer Patients ◽  
Variant Calling ◽  
Batch Effect ◽  
Cancer Predisposition ◽  
The Cancer Genome Atlas ◽  
Batch Effects ◽  
Germline Variants ◽  
Predisposition Genes ◽  
Cancer Types ◽  
Pan Cancer

ABSTRACTBackgroundIn recent years, research on cancer predisposition germline variants has emerged as a prominent field. The identity of somatic mutations is based on a reliable mapping of the patient germline variants. In addition, the statistics of germline variants frequencies in healthy individuals and cancer patients is the basis for seeking candidates for cancer predisposition genes. The Cancer Genome Atlas (TCGA) is one of the main sources of such data, providing a diverse collection of molecular data including deep sequencing for more than 30 types of cancer from >10,000 patients.MethodsOur hypothesis in this study is that whole exome sequences from healthy blood samples of cancer patients are not expected to show systematic differences among cancer types. To test this hypothesis, we analyzed common and rare germline variants across six cancer types, covering 2,241 samples from TCGA. In our analysis we accounted for inherent variables in the data including the different variant calling protocols, sequencing platforms, and ethnicity.ResultsWe report on substantial batch effects in germline variants associated with cancer types. We attribute the effect to the specific sequencing centers that produced the data. Specifically, we measured 30% variability in the number of reported germline variants per sample across sequencing centers. The batch effect is further expressed in nucleotide composition and variant frequencies. Importantly, the batch effect causes substantial differences in germline variant distribution patterns across numerous genes, including prominent cancer predisposition genes such as BRCA1, RET, MAX, and KRAS. For most of known cancer predisposition genes, we found a distinct batch-dependent difference in germline variants.ConclusionTCGA germline data is exposed to strong batch effects with substantial variabilities among TCGA sequencing centers. We claim that those batch effects are consequential for numerous TCGA pan-cancer studies. In particular, these effects may compromise the reliability and the potency to detect new cancer predisposition genes. Furthermore, interpretation of pan-cancer analyses should be revisited in view of the source of the genomic data after accounting for the reported batch effects.

scholarly journals Germline cancer predisposition variants and pediatric glioma: a population-based study in California

2020 ◽  
Vol 22 (6) ◽  
pp. 864-874 ◽  
Author(s):  
Ivo S Muskens ◽  
Adam J de Smith ◽  
Chenan Zhang ◽  
Helen M Hansen ◽  
Libby Morimoto ◽  
...  
Keyword(s):  
Cell Cycle Control ◽  
Population Level ◽  
Cancer Predisposition ◽  
Sequencing Data ◽  
Pediatric Glioma ◽  
Germline Variants ◽  
Pathogenic Variants ◽  
Predisposition Genes ◽  
Pediatric Astrocytoma ◽  
Pediatric Glioblastoma

Abstract Background Pediatric astrocytoma constitutes a majority of malignant pediatric brain tumors. Previous studies that investigated pediatric cancer predisposition have primarily been conducted in tertiary referral centers and focused on cancer predisposition genes. In this study, we investigated the contribution of rare germline variants to risk of malignant pediatric astrocytoma on a population level. Methods DNA samples were extracted from neonatal dried bloodspots from 280 pediatric astrocytoma patients (predominantly high grade) born and diagnosed in California and were subjected to whole-exome sequencing. Sequencing data were analyzed using agnostic exome-wide gene-burden testing and variant identification for putatively pathogenic variants in 175 a priori candidate cancer-predisposition genes. Results We identified 33 putatively pathogenic germline variants among 31 patients (11.1%) which were located in 24 genes largely involved in DNA repair and cell cycle control. Patients with pediatric glioblastoma were most likely to harbor putatively pathogenic germline variants (14.3%, N = 9/63). Five variants were located in tumor protein 53 (TP53), of which 4 were identified among patients with glioblastoma (6.3%, N = 4/63). The next most frequently mutated gene was neurofibromatosis 1 (NF1), in which putatively pathogenic variants were identified in 4 patients with astrocytoma not otherwise specified. Gene-burden testing also revealed that putatively pathogenic variants in TP53 were significantly associated with pediatric glioblastoma on an exome-wide level (odds ratio, 32.8, P = 8.04 × 10−7). Conclusion A considerable fraction of pediatric glioma patients, especially those of higher grade, harbor a putatively pathogenic variant in a cancer predisposition gene. Some of these variants may be clinically actionable or may warrant genetic counseling.

scholarly journals Cell-free Circulating Tumor DNA Variant Allele Frequency Associates with Survival in Metastatic Cancer

2019 ◽  
Vol 26 (8) ◽  
pp. 1924-1931 ◽  
Author(s):  
Seyed Pairawan ◽  
Kenneth R. Hess ◽  
Filip Janku ◽  
Nora S. Sanchez ◽  
Kenna R. Mills Shaw ◽  
...  
Keyword(s):  
Allele Frequency ◽  
Metastatic Cancer ◽  
Circulating Tumor Dna ◽  
Variant Allele ◽  
Variant Allele Frequency ◽  
Tumor Dna

scholarly journals Cancer Predisposition Sequencing Reporter (CPSR): a flexible variant report engine for high-throughput germline screening in cancer

2019 ◽  
Author(s):  
Sigve Nakken ◽  
Vladislav Saveliev ◽  
Oliver Hofmann ◽  
Pål Møller ◽  
Ola Myklebost ◽  
...  
Keyword(s):  
High Throughput ◽  
Association Studies ◽  
Treatment Strategies ◽  
Cancer Predisposition ◽  
Genome Wide Association Studies ◽  
Germline Variants ◽  
Pathogenic Variants ◽  
Risk Variants ◽  
The Status ◽  
Predisposition Genes

AbstractThe value of high-throughput germline genetic testing is increasingly recognized in clinical cancer care. Disease-associated germline variants in cancer patients are important for risk management and surveillance, surgical decisions, and can also have major implications for treatment strategies since many are in DNA repair genes. With the increasing availability of high-throughput DNA sequencing in cancer clinics and research, there is thus a need to provide clinically oriented sequencing reports for germline variants and their potential therapeutic relevance on a per-patient basis. To meet this need we have developed the Cancer Predisposition Sequencing Reporter (CPSR), an open-source computational workflow that generates a structured report of germline variants identified in known cancer predisposition genes, highlighting markers of therapeutic, prognostic, and diagnostic relevance. A fully automated variant classification procedure based on more than 30 refined ACMG criteria represents an integral part of the workflow. Importantly, the set of cancer predisposition genes profiled in the report can be flexibly chosen from more than 40 virtual gene panels established by scientific experts, enabling customization of the report for different screening purposes and clinical contexts. The report can be configured to also list actionable secondary variant findings as recommended by ACMG, as well as the status of low-risk variants from genome-wide association studies in cancer. CPSR demonstrates superior sensitivity and comparable specificity for the detection of pathogenic variants when compared to existing algorithms. Technically, the tool is implemented in Python/R, and is freely available through Docker technology. Source code, documentation, example reports, and installation instructions are accessible via the project GitHub page: https://github.com/sigven/cpsr.

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