Somatic Single Nucleotide Variants Research Articles

Clinical and genomic features of non-small cell lung cancer occurring in families.

Exposure to environmental carcinogens, such as through smoking, is a major factor in the carcinogenesis of non-small cell lung cancer (NSCLC). However, genetic factors may also contribute. To identify candidate tumor suppressor genes for NSCLC, we included 23 patients (10 related pairs and 3 individuals) with NSCLC who had other NSCLC-affected first-degree relatives in a local hospital. Exome analyses for both germline and somatic (NSCLC specimens) DNA were performed for 17 cases. Germline exome data of these 17 cases revealed that most of the short variants were identical to the variants in 14KJPN (a Japanese reference genome panel of more than 14 000 individuals) and only a nonsynonymous variant in the DHODH gene, p.A347T, was shared between a pair of NSCLC patients in the same family. This variant is a known pathogenic variant of the gene for Miller syndrome. Somatic genetic alterations in the exome data of our samples showed frequent mutations in the EGFR and TP53 genes. Principal component analysis of the patterns of 96 types of single nucleotide variants (SNVs) suggested the existence of unique mechanisms inducing somatic SNVs in each family. Delineation of mutational signatures of the somatic SNVs with deconstructSigs for the pair of germline pathogenic DHODH variant-positive cases showed that the mutational signatures of these cases included SBS3 (homologous recombination repair defect), SBS6, 15 (DNA mismatch repair), and SBS7 (ultraviolet exposure), suggesting that disordered pyrimidine production causes increased errors in DNA repair systems in these cases. Our results suggest the importance of the detailed collection of data on environmental exposure along with genetic information on NSCLC patients to identify the unique combinations that cause lung tumorigenesis in a particular family.

Minimal residual disease detection by mutation-specific droplet digital PCR for leukemia/lymphoma

Minimal residual disease (MRD) is usually defined as the small number of cancer cells that remain in the body after treatment. The clinical significance of MRD kinetics is well recognized in treatment of hematologic malignancies, particularly acute lymphoblastic leukemia (ALL). Real time quantitative PCR targeting immunoglobulin (Ig) or T-cell receptor (TCR) rearrangement (PCR-MRD), as well as multiparametric flow cytometric analysis targeting antigen expression, are widely used in MRD detection. In this study, we devised an alternative method to detect MRD using droplet digital PCR (ddPCR), targeting somatic single nucleotide variants (SNVs). This ddPCR-based method (ddPCR-MRD) had sensitivity up to 1E-4. We assessed ddPCR-MRD at 26 time points from eight T-ALL patients, and compared it to the results of PCR-MRD. Almost all results were concordant between the two methods, but ddPCR-MRD detected micro-residual disease that was missed by PCR-MRD in one patient. We also measured MRD in stored ovarian tissue of four pediatric cancer patients, and detected 1E-2 of submicroscopic infiltration. Considering the universality of ddPCR-MRD, the methods can be used as a complement for not only ALL, but also other malignant diseases regardless of tumor-specific Ig/TCR or surface antigen patterns.

Abstract P2-26-06: Association between CK+/CD45+ circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) alterations in advanced breast cancer patients

Abstract Background: Circulating tumor cells (CTCs) in breast cancer (BC) are commonly defined as epithelial cells (EPCAM and cytokeratin (CK) positive), lacking the universal blood cell marker CD45. Nonetheless, CTCs expressing both CK and CD45 (= dual-positive, DP cells) can be observed in the blood of cancer patients. Early evidence suggests that DP cells might derive from the fusion of tumor cells and macrophages, and we have previously demonstrated that they present aberrant genomes and are associated with worse prognosis in BC [1,2]. Here, to further investigate the mechanisms/pathways underlying their presence, we analyzed the association between DP cells and circulating tumor DNA (ctDNA) alterations. Methods: Blood samples were collected from patients with advanced BC (aBC), before starting a new line of therapy. All patients were enrolled in a prospective clinical trial. For CTC and DP cells analysis, 7.5 ml of blood collected in CellSave® tubes was processed with the FDA-approved CellSearch® platform (positivity cutoffs were ≥1 cell for DPcells and ≥5 cells for CTCs). For ctDNA analysis, plasma was collected from Streck stabilizing tubes and analyzed with the Guardant360™ NGS platform for the detection of somatic single nucleotide variants (SNVs), insertions/deletions (indels), gene fusions/rearrangements and copy number variations (CNVs), which were then classified into pathways based on previously defined profiles generated on the Cancer Genome Atlas database (RTK, RAS, RAF, MEK, NRF2, ER, WNT, MYC, P53, cell cycle, notch, PI3K). Associations between ctDNA-detected gene alterations and circulating cell types were analyzed through chi square test, while mutant allele frequency (MAF) and number of detected alterations (NDA) were tested by Mann Whitney test. Results: We analyzed blood samples from 169 patients with luminal-like (n=80), HER2+ (n=34) and triple-negative (n=52) aBC. DPcells were detected in 85 patients (50.3 %, range 0-53), of which 40 (47 %) were CTC-positive and 45 (53%) CTC-negative. Somatic ctDNA alterations were detected in all analyzed samples. In the overall population, the presence of ≥1 DPcell was associated with SNVs in the cell cycle pathway (p = 0.043), a numerically higher incidence was also observed for CNVs in this pathway. SNVs and CNVs in the cell cycle pathway were associated with CTCs ≥ 5 as well (p = 0.005 and p = 0.003, respectively). Moreover, associations with CTCs ≥ 5 were observed for RTK SNVs and CNVs (p = 0.041 and p = 0.046, respectively), PI3K SNVs and CNVs (p = 0.006 and p = 0.007, respectively), MYC SNVs and CNVs (p = 0.042). No associations were observed in terms of MAF and NDA. In the luminal-like subgroup an association was highlighted for CNVs in the cell cycle pathway, p = 0.038. CTCs ≥ 5 were associated with PI3K SNVs (p = 0.031). In the triple-negative subgroup DPcells were associated with SNVs in the RAF pathway (p = 0.041), whereas CTCs ≥ 5 were associated with PI3K SNVs and CNVs (p = 0.044 and p = 0.024, respectively) and RTK SNVs (p = 0.008). In the HER2 positive subgroup, a higher MAF and number of detected SNVs was observed for samples with ≥1 DPcell (p = 0.0286 and p = 0.0099, respectively). Conclusions: The study analyzed ctDNA features associated with canonical and CK+/CD45+ CTCs, showing differential gene alteration profiles. Cell cycle pathway SNVs were common in both CTC populations, while other pathways (RTK, PI3K, MYC and RAF) were significantly altered in a mutually exclusive pattern. These results suggest that DPcells might have a different biological meaning compared to canonical CTCs. More studies need to be conducted to better characterize this understudied CTC subpopulation and understand their specific contribution to cancer progression.

Abstract P5-02-24: Whole genome sequencing of long-term, never relapse exceptional responders HER2+ advanced metastatic breast cancer

Abstract Background: Anti-HER2 therapies such as trastuzumab used for the treatment of patients with HER2+ metastatic breast cancer (MBC) have led to significant improvements to disease progression. We previously identified cases from the “Thousand Patient HER2 database” project at Saint Vincent’s University Hospital (SVUH) Dublin, of HER2+ MBC long-term durable complete responders to trastuzumab, and reported that Copy Number Aberration (CNA) burden may represent a novel prognostic predictor to trastuzumab response from the exome analysis of in HER2+ MBC “exceptional responders’’ (ExRs). However, whole-genome sequencing (WGS) allows a better understanding of how CNA affects the MBC genome and to-date, the complete genome of this “exceptional” cohort has never been described. Methods: We performed WGS analysis to characterise the CNA profiles of 9 ExRs from our HER2+ MBC cohort treated with trastuzumab. Samples were obtained from patients who never progressed/relapsed for more than 5 years (OS > 60 months). DNA was sequenced from tumours (primary or metastases) and matching control (blood or normal tissue) at a mean depth of 60X and 30X, respectively (18 samples). Somatic single nucleotide variants (SNV) were detected using GATK4 Mutect2 and CNA were identified using Control-FREEC. Results: Eighty-five HER2+ MBC were identified with OS > 60 months, of which 28 were ExRs with bone, lung, liver and lymph metastasis who responded exceptionally to trastuzumab, with a mean OS of 108 months (range 61-236 months). This cohort includes patients who were diagnosed between 31 and 80 years old (median=51). WGS analysis revealed CNA in chr6p21 with amplification of CCND3 and in chr17q12 with amplification of RAD51D. SNV were identified in genes involved in the DNA damage repair (DDR) pathway such as ATM, BRCA2, RAD50 and FANCA. On-going analysis will allow the CNA profiles of all ExRs to be presented and their CNA burden calculated in order to investigate the relationship between whole genome CNA burden and HER2+ MBC patient survival. Conclusion: To our knowledge, this is the first study to sequence the whole genome of HER2+ MBC, never relapse exceptional responders. The identification of the genomic aberrations of these metastatic patients increases our understanding of the mechanisms involved in MBC progression. CNA burden may represent a novel prognostic predictor to trastuzumab response and new outcomes for patients, particularly as MBC is generally termed incurable. Citation Format: Charlotte Andrieu, Laura P. Ivers, Jose Javier Berenguer Pina, Darko Skrobo, Jo Ballot, Alex J. Eustace, Cecily Quinn, Giuseppe Gullo, Naomi Walsh, John P. Crown. Whole genome sequencing of long-term, never relapse exceptional responders HER2+ advanced metastatic breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-02-24.

Abstract P2-23-15: Histologic, immunohistochemical and genomic comparison between classic Invasive lobular carcinomas and lobular-like invasive ductal carcinomas

Abstract Background: Invasive lobular carcinomas (ILCs) are the most frequent special histologic subtype of breast cancer, accounting for up to 15% of all breast cancer cases. ILCs are characterized by a distinctive discohesive growth pattern, with cells arranged in single cell infiltrative file and dispersed throughout the stroma, which stems from the loss of E-cadherin expression due to bi-allelic inactivation of the CDH1 gene. A subset of breast cancers display a similar single cell infiltrative growth pattern but, in contrast to classic ILC, display diffuse strong membranous E-cadherin reactivity and membranous p120 expression. We refer to such cases as “lobular-like invasive ductal carcinoma” (LLIDC), but it is unclear if this terminology is appropriate and if such cases show biallelic inactivation of CDH1, similarly to ILCs. Here, we sought to define whether LLIDCs would harbor bi-allelic alterations of CDH1 and to perform an exploratory, hypothesis generating analysis of the repertoire of somatic genetic alterations of LLIDCs and classic ILCs. Materials and methods: Representative H&Es, as well as sections subjected to E-cadherin and p120 immunohistochemistry from seven classic ILCs and seven bona fide “lobular-like invasive ductal carcinomas” were retrieved and independently reviewed by two pathologists with experience and expertise in breast pathology. DNA samples were extracted from representative sections from tumor and normal breast tissue from each patient and subjected to an FDA-approved targeted sequencing assay comprising the coding regions and selected regulatory elements of 515 genes. Somatic single nucleotide variants (SNVs) were detected with MuTect, indels with Strelka, Varscan2, Scalpel and Lancet. All mutations were manually inspected using the Integrative Genomics Viewer (IGV). The cancer cell fraction (CCF) of each mutation was inferred, as well as clonal probability, using ABSOLUTE. Copy number alterations and loss of heterozygosity were determined using FACETS. Mutational signatures were inferred using SigMA based on all synonymous and nonsynonymous somatic mutations. Results: Based on the histopathologic evaluation, of the 14 cases analyzed, seven were classified as ILC, and the other seven were classified as LLIDC. Sequencing analysis revealed that the classic ILCs harbored 16q LOH and CDH1 mutations (7/7), of which five were frameshift indel and two were splice site mutations consistently coupled with loss-of-heterozygosity (LOH) of the wild-type allele. Conversely, five of the seven LLIDCs did not harbor CDH1 mutations or genomic rearrangements. CDH1 mutations were identified in 2 LLIDCs: one harbored a subclonal CDH1 in-frame indel mutation coupled with LOH. This case displayed membranous E-cadherin and p120 expression with areas of aberrant expression. The other CDH1-mutated LLIDC harbored a complex in-frame indel with subclonal LOH. This case displayed membranous E-cadherin and p120 expression. The comparative analysis of the repertoire of somatic genetic alterations and mutational signatures present in LLIDCs and classic ILCs did not reveal any significant differences. Conclusion: Despite the histologic similarities, LLIDCs differ from classic lobular carcinomas based on the lack of CDH1 bi-allelic inactivation and the patterns of expression of E-cadherin and p120 catenin. Further whole-genome sequencing analyses are warranted to define the molecular basis of the discohesive cancer cells of LLIDC display. Citation Format: Edaise M. da Silva, Thais Basili, Jing Yu, Juan Blanco-Heredia, Pier Selenica, Qiqi Ye, Arnaud da Cruz Paula, Higinio Dopeso, Antonio Marra, Steffi Oesterreich, Jorge Reis-Filho, Rohit Bhargava. Histologic, immunohistochemical and genomic comparison between classic Invasive lobular carcinomas and lobular-like invasive ductal carcinomas [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-23-15.

Abstract P5-02-22: Circulating Tumor DNA Genotyping of Intrinsic and Acquired Gene Alterations in Patients With Advanced Breast Cancer Receiving the Cyclin-Dependent Kinase 4/6 Inhibitor Palbociclib: Biomarker Results from POLARIS

Abstract Background: POLARIS is a prospective, real-world study of palbociclib in patients with hormone receptor–positive (HR+)/human epidermal growth factor receptor 2–negative (HER2–) advanced breast cancer (ABC) in the United States and Canada. We present results from analyses of serial circulating tumor gene alteration profiles from patients treated with palbociclib in the first and second or later lines of ABC treatment to illustrate the potential mutagenic drivers of resistance (intrinsic/acquired) and carrier-mutations (intrinsic/maintained). Methods: The clinical database cutoff date was March 30, 2022. Patients in the biomarker analysis group provided consent for serial blood sample collection, received ≥1 dose of initial palbociclib combination treatment, and had ≥1 circulating tumor DNA (ctDNA) measurement available. The Guardant360 platform with somatic single-nucleotide variants in complete or critical exons of 73 genes was used. Tumor gene alteration profiles (at baseline, on-treatment at Cycle 2 Day 1 [C2D1], and at end of treatment [EOT]) were evaluated. Cox proportional hazard models were used to estimate hazard ratios and 95% CIs. Results: Patient samples (n=345) were analyzed and gene alterations were detected in 85% of baseline samples (n=337), 72% of on-treatment samples (n=280), and 85% of EOT samples (n=104). Most frequently altered genes were PIK3CA (38%), TP53 (28%), and ESR1 (15%) at baseline; TP53 (28%), PIK3CA (24%), and NF1 (10%) at C2D1; and TP53 (40%), PIK3CA (40%), and ESR1 (33%) at EOT. Most frequent gene amplifications (amp) were detected in CCND1 (8.3%), FGFR1 (7.7%), and EGFR (5.9%) at baseline; FGFR1 (5.0%), CCND1 (4.3%), and EGFR (3.2%) at C2D1; and CCND1 (13.5%), FGFR1 (9.6%), and EGFR (9.6%) at EOT. Baseline mutations of ESR1 and PIK3CA led to shorter real-world progression-free survival (rwPFS) than wild-type (hazard ratio [95% CI], 1.99 [1.38, 2.86] and 1.67 [1.24, 2.25], respectively). Baseline amp of CCND1 and FGFR1 also led to shorter rwPFS than wild-type (2.13 [1.36, 3.34] and 1.93 [1.20, 3.10]). Acquired mutations in ESR1, ATM, and RB1 were observed at EOT. Most frequently acquired ESR1 mutations at EOT were D538G, Y537N, and Y537S. Patients with all mutations cleared at C2D1, had longer rwPFS than those without (hazard ratio [95% CI], 0.58 [0.41, 0.83]). Conclusion: Patients with mutated ESR1 and PIK3CA or CCND1 and FGFR1 amp at baseline had shorter rwPFS than patients with wild-type genes. Genotyping analysis of progression ctDNA highlights the emergence of mutations in estrogen receptor and cell cycle pathways under selective therapeutic pressure and could guide monitoring and therapeutic sequencing for patients with HR+/HER2– MBC. ClinicalTrials.gov: NCT03280303 Citation Format: Debu Tripathy, Joanne L. Blum, Shibing Deng, Steven L. McCune, Kamal Patel, Yao Wang, Shailendra Lakhanpal, Meghan S. Karuturi, Zhe Zhang, Chetan Deshpande, Monica Z. Montelongo, Eric Gauthier, Yuan Liu, Gabrielle B. Rocque, Aditya Bardia. Circulating Tumor DNA Genotyping of Intrinsic and Acquired Gene Alterations in Patients With Advanced Breast Cancer Receiving the Cyclin-Dependent Kinase 4/6 Inhibitor Palbociclib: Biomarker Results from POLARIS [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-02-22.

Abstract PD17-02: ctDNA Molecular Response based on breast cancer driver mutations predicts progression in aromatase inhibitor-sensitive first line treatment of oestrogen receptor-positive (ER+) HER2-negative (HER2-) advanced breast cancer

Abstract Background: The combination of a CDK4/6 inhibitor and an aromatase inhibitor (AI) is the gold standard for AI-sensitive first line treatment of ER+ HER2- advanced breast cancer. Nevertheless, some patients progress rapidly and may benefit from alternative strategies. Early ctDNA dynamics have been shown to predict disease course in several clinical situations. Here, we use samples from the PADA-1 trial to assess this strategy for patients receiving AI and palbociclib as first line treatment. PADA-1 was designed to assess the clinical utility of sequential analysis of ctDNA for emerging ESR1 mutations to trigger an early switch from AI plus palbociclib to fulvestrant plus palbociclib treatment. The study included 1,017 patients and was positive on its primary end-point. The objective of this translational study was to analyze the predictive value of 4-week molecular response (MR) for patient progression. Material & Method: First, a CLIA-validated targeted next-generation sequencing-based test (Guardant360 Response) was used to characterize changes in ctDNA level via detection of somatic single-nucleotide variants (SNVs), insertion/deletion mutations (indels), and gene fusions in 74 genes frequently mutated in cancer. A second analysis was restricted to cancer-associated mutations in 11 genes commonly mutated in breast cancer (PIK3CA, GATA3, TP53, AKT1, ERBB2, BRCA1, BRCA2, ATM, ESR1, PALB2 and RB1). The threshold for molecular response was defined as ≥ 50% decrease in ctDNA (MR score < 0.5). Subjects with ctDNA levels below the test’s limit of quantitation (ctDNA-low) were considered molecular responders. Results: 372 subjects with matched baseline and 4-weeks samples were available for analysis. Of these, 134 subjects (36%) were ctDNA-low, and 238 subjects (64%) quantifiable. Among the quantifiable subjects, 183 (77%) were molecular responders (MR+, MR < 0.5), and 55 (23%) were not (MR–, MR ≥ 0.5). PFS was moderately improved for both MR+ and ctDNA-low relative to MR– (HR=0.61 (95%CI 0.44-0.85), p< 0.01) over the full 29 months of follow up. Differential PFS event rate was observed only in the first 8 months following ctDNA assessment; during this time MR+ and ctDNA-low were associated with more significantly decreased risk of progression (HR 0.24, 95% CI 0.13 – 0.43, p=0.0001). Limiting ctDNA assessment to genes commonly mutated in breast cancer enhanced the predictive power of MR (HR=0.08, 95% CI 0.04 0.17, p< 0.001, for MR+ and ctDNA-low vs. MR– across 8 months post-assessment); however, fewer samples were quantifiable by this method (169 [45%] quantifiable; 203 [55%] ctDNA-low). Combining MR status with additional molecular features (e.g.tumor mutational burden and maximum mutation allele fraction) did not improve prediction of non-response. Conclusion: Changes in ctDNA fraction during the first weeks of treatment are predictive of long term clinical benefit on an individual patient basis, particularly during the first year of therapy. Adjusting the MR threshold and/or limiting to genes known to be relevant in the specific tumor can tailor the assessment of ctDNA change to specific clinical scenarios where greater sensitivity or specificity may be required. The identification of patients at high risk for early clinical failure at the onset of treatment may allow for therapy escalation and/or change to improve outcome in this population. Funding: Pfizer and Guardant Health Citation Format: Caroline Bailleux, Thomas Bachelot, Francois-Clement Bidard, Anne-Claire Hardy-Bessard, Ivan Bièche, Anne Pradines, Florian Clatot, thibault DE LA MOTTE ROUGE, Jean-Luc Canon, Barbara Pistilli, Kyle Chang, Katie J. Quinn, Heather L. Gustafson, Florence Dalenc, Cyril Foa, Hanifa Ammarguellat, Chantal Bernard-Marty, Brigitte Lucas, Sophie Barthier, Fabrice Lorchel, Olivier Gisserot, Laurent Arnould, Marjorie Mauduit, Jérôme Lemonnier, Frédérique Berger, Suzette Delaloge, Fabrice Andre. ctDNA Molecular Response based on breast cancer driver mutations predicts progression in aromatase inhibitor-sensitive first line treatment of oestrogen receptor-positive (ER+) HER2-negative (HER2-) advanced breast cancer. [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD17-02.

Somatic Variants and Exon-Level Copy Number Changes in Five Hyperplastic Oral Leukoplakias

Oral leukoplakia (OL), an oral potentially malignant disorder, begins with a hyperplastic/hyperkeratotic stage at which no genome-scale somatic single nucleotide variant profiles have been described so far. We performed exome sequencing of five cases at this stage with no evidence of dysplasia to identify genetic alterations (exon-level copy number alterations, indels, and single nucleotide variants), their association with transcript levels, and relationship with oral cancer susceptibility. Pathway enrichment analysis of genes associated with tobacco chewing and age-related mutation signatures, transcripts with variants predicted to be functionally damaging and those with significantly altered levels all indicated the involvement of focal adhesion, ECM-receptor interactions, regulation of cytoskeleton, and DNA repair. Two novel mutations identified in FAT1 tumor suppressor gene were associated with decreased transcript levels. In addition, 16 expressed cancer driver genes contained functionally damaging variants. Many of the affected genes were also reported in dysplastic OL lesions. The presence of variants in cancer driver genes and those shared with oral dysplasias possibly provides a basis for further progression and increased susceptibility to oral cancer.

Mutational Landscape of Bladder Cancer in Mexican Patients: KMT2D Mutations and chr11q15.5 Amplifications Are Associated with Muscle Invasion.

Bladder cancer (BC) is the most common neoplasm of the urinary tract, which originates in the epithelium that covers the inner surface of the bladder. The molecular BC profile has led to the development of different classifications of non-muscle invasive bladder cancer (NMIBC) and muscle-invasive bladder cancer (MIBC). However, the genomic BC landscape profile of the Mexican population, including NMIBC and MIBC, is unknown. In this study, we aimed to identify somatic single nucleotide variants (SNVs) and copy number variations (CNVs) in Mexican patients with BC and their associations with clinical and pathological characteristics. We retrospectively evaluated 37 patients treated between 2012 and 2021 at the National Cancer Institute-Mexico (INCan). DNA samples were obtained from paraffin-embedded tumor tissues and exome sequenced. Strelka2 and Lancet packages were used to identify SNVs and insertions or deletions. FACETS was used to determine CNVs. We found a high frequency of mutations in TP53 and KMT2D, gains in 11q15.5 and 19p13.11-q12, and losses in 7q11.23. STAG2 mutations and 1q11.23 deletions were also associated with NMIBC and low histologic grade.

Single-neuron whole genome sequencing identifies increased somatic mutation burden in Alzheimer's disease related genes

Accumulation of somatic mutations in human neurons is associated with aging and neurodegeneration. To shed light on the somatic mutational burden in Alzheimer's disease (AD) neurons and get more insight into the role of somatic mutations in AD pathogenesis, we performed single-neuron whole genome sequencing to detect genome-wide somatic mutations (single nucleotide variants (SNVs) and Indels) in 96 single prefrontal cortex neurons from 8 AD patients and 8 elderly controls. We found that the mutational burden is ∼3000 somatic mutations per neuron genome in elderly subjects. AD patients have increased somatic mutation burden in AD-related annotation categories, including AD risk genes and differentially expressed genes in AD neurons. Mutational signature analysis showed somatic SNVs (sSNVs) primarily caused by aging and oxidative DNA damage processes but no significant difference was detected between AD and controls. Additionally, functional somatic mutations identified in AD patients showed significant enrichment in several AD-related pathways, including AD pathway, Notch-signaling pathway and Calcium-signaling pathway. These findings provide genetic insights into how somatic mutations may alter the function of single neurons and exert their potential roles in the pathogenesis of AD.

Single‐Neuron Genome Sequencing in Alzheimer’s Disease Identifies Disease‐Specific Somatic Alterations and Insights into Pathogenesis

AbstractBackgroundAlzheimer’s disease (AD) is characterized pathologically by deposition of misfolded amyloid‐b and tau proteins. However, protein‐directed therapeutic strategies have shown limited clinical benefit, pointing to the need to examine pathogenesis from a broader lens.Neurons each harbor somatic single nucleotide variants (sSNV) in their genomes, which increase with age, at a rate of ∼15 sSNV per year. In AD, DNA damage is increased, with potentially significant effects on the genome of each cell.MethodWe performed single‐cell whole‐genome sequencing on neurons from postmortem brain tissue from humans with AD and age‐matched controls, using two independent genome amplification methods (MDA and PTA), and analyzed the burden of somatic mutations. We also performed mutational signature analysis of the nucleotide changes and trinucleotide context to assess for mutagenic patterns.ResultWe found significantly increased sSNV in AD, with each neuron carrying hundreds of additional somatic mutations, with a distinct mutation pattern. AD neurons show an increase in Signature C, which contains distinct nucleotide changes including C>A variants. We found elevated 8‐Oxoguanine DNA lesions, evidence that these mutations may result from oxidative damage to DNA. Mutations also show a mechanistic role for gene transcription in the generation of sSNV. Somatic mutations are predicted to produce deleterious effects on the neuron, including gene inactivation and neoantigen‐stimulated immune attack.ConclusionSomatic mutations accumulate abundantly in Alzheimer’s disease, distributed across the genome. Our findings implicate multiple mutagenic forces in sSNV generation in AD, illuminating multiple upstream components of disease pathogenesis including DNA oxidation and transcription‐coupled DNA repair. Furthermore, elevated somatic mutation levels appear to produce a toxic cellular state, positioning neurons for dysfunction and death. These findings therefore identify somatic mutation accumulation as a novel process in neurodegeneration, through which we can dissect the cascade of events in Alzheimer’s disease pathogenesis.

Temporal and spatial characteristics of tumor evolution in a mouse model of oral squamous cell carcinoma

ObjectivesWe aimed to elucidate the temporal and spatial characteristics of tumor evolution in an oral squamous cell carcinoma (OSCC) mouse model with higher burden of lymphatic metastasis through high-throughput sequencing.MethodsThe OSCC model was established in 9 mice. DNA was extracted from the tumors of primary tongue lesions and disseminated tumor cells (DTCs) of submandibular gland lymph nodes and bone marrow, and then whole genome sequencing was performed. After bioinformatics analysis, somatic single-nucleotide variants (SSNVs) and copy number variations (CNVs) data were obtained. Based on SSNVs, clonal architecture and ancestor-descendant relationships among tumor cell subclones were elucidated.ResultsA total of 238 tumor-related SSNVs with 120 high-frequency mutated genes were obtained from 36 samples of 9 mice by whole-genome sequencing. The number of unique SSNVs in the primary lesion, submandibular lymph node and bone marrow was greater than the number of shared SSNVs. Furthermore, the primary lesion-originated subclones, which were identified by SSNVs, were also detected in submandibular lymph nodes in the early stage of oral carcinogenesis. Moreover, at different histopathological stages, unique subclones were also identified in DTCs isolated from lymph nodes.ConclusionTumor heterogeneity is significant in primary tumor cells and disseminated tumor cells. OSCC cells probably disseminate to lymph nodes in the early stage of oral carcinogenesis. OSCC is characterized by polyclonal dissemination, and the evolutionary trajectory of DTCs is potentially dominated by the tumor microenvironment.

Identification and Interpretation of Clinically Relevant Somatic Variants from Whole-Genome Sequencing Data

Whole-genome sequencing provides an opportunity for a comprehensive test enabling detection of clinically relevant genetic aberrations for patients with hematological malignancies. However in diagnostic settings, it is challenging to identify and interpret clinically relevant somatic single nucleotide variants (SNV), small insertions and deletions (INDEL), structural variants (SV) and copy-number variants (CNV) in a manner that retains the sensitivity of the analysis while at the same time enabling a rapid interpretation. SNV and INDEL are identified using the information from within the sequenced reads, and range in size smaller than 10 bp. Both SV and CNV are typically longer than 100 bp and are identified using different properties from aligned reads, which includes split reads, and orientation and distance between the read pairs. These aberrations are further divided into different categories depending upon their complexity and the method of identification, which include duplications (DUP), deletions (DEL), inversions (INV) and translocation breakpoints (BND). Although CNV is defined as an additional type of variant, the copy number gains and losses, identified using read-depth profile, can be categorized as DUP and DEL. All four types of SV arise due to complex rearrangements in the genome. Their inherent complexity combined with the methods used to identify them makes it difficult to obtain a comprehensive set of true biological events. Furthermore, identification of clinically relevant somatic variants requires further classification of all variants into germline and somatic using additional variant-type dependent processing and filtering. Finally, to enable rapid processing that meets the clinical diagnostic demands regarding turnaround times, the entire process needs to be automated with minimum human intervention from sample preparation and bioinformatic analysis all the way through clinical interpretation. To tackle these challenges, we implemented an ensemble variant calling approach in BALSAMIC. This involves combining computational methods and tools to identify SNV, INDEL and all four types of SV. These variants are then subjected to further bioinformatic processing and rigorous filtering to prepare them for clinical interpretation in our custom-developed variant interpretation software, Scout. The entire workflow is automated using in-house automation software, cg. BALSAMIC utilizes FASTQ files as input and first performs quality control and trimming using FastQC and fastp, respectively. Trimmed reads are mapped to the human reference genome using Sentieon-tools. Duplicated reads are marked and quality controlled using Picard-tools and the results are summarized by MultiQC. SNV and INDEL are called using Sentieon TNscope and TNhaplotyper. The variants are further processed using depth, quality and allele frequency based filters. The filtered SNV and INDEL from TNscope and Tnhaplotyper are merged using bcftools for tumor-only samples. Manta, Delly-SV, and TIDDIT are used to call SV while ascatNgs (tumor-normal) and Delly-CNV are used to call CNV. CNV calls are further converted from CNV to DEL and DUP to curate merged sets for each SV-type across the different SV-callers. The SV calls from Manta, Delly, TIDDIT, and ascatNgs (tumor-normal) are then merged using SVDB. Prior to annotation, SVs with low quality score in the tumor sample, high allelic frequency (possible germline) in the normal sample, or longer than 10Mb are removed. Next, SVs are annotated using Ensembl-VEP and the variants in the intragenic regions are removed. Finally, SVs are uploaded to Scout and those overlapping with clinically relevant genes (defined using an in silico gene list) constitute the final set of clinically relevant somatic SNV, INDEL, SV and CNV. This workflow has analyzed to date more than two hundred cases of different tumor types mainly including hematological malignancies. This approach identifies thousands of variants across all types, but with rigorous processing and filtering, the identification of clinically relevant somatic variants is done in a manner compatible with the clinical diagnostic demands. Software availability The bioinformatics software BALSAMIC, cg and Scout are available from https://github.com/Clinical-Genomics, and the details of the software and methods used in BALSAMIC are available from https://balsamic.readthedocs.io. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Mutational Mechanisms in Pediatric Acute Lymphoblastic Leukemia with Multiple Relapses

Pediatric acute lymphoblastic leukemia (ALL) is generally marked by a low mutational load at initial diagnosis, which increases in subsequent relapses, partly because of hypermutation in a subset of cases (Waanders et al., 2020, Blood Canc. Disc., 1:96). This increased mutational load can be driven by intrinsic mutational processes or could be therapy related. In this study, we have investigated these mutational processes in pediatric ALL patients who suffered multiple relapses, to determine which processes are active in (relapsed) ALL and how they behave during disease progression before and after therapy. We identified 63 historical cases of ALL with multiple relapses, and selected patients by availability of material and blast percentage above 70% in multiple leukemic samples. If viable material with less than 70% blasts was available, mononuclear cells were enriched by sorting for CD10 positivity. We collected and whole genome sequenced 97 tumor samples from 28 ALL patients (27 precursor B-ALL and 1 T-ALL) with 2 (n=17) or more (n=11) relapses, and 44 remission samples. Somatic single nucleotide variants (SNVs) were called by Mutect2. SNVs were clustered per sample based on their dynamics in time and all clusters in all patients were included for de novo signature extraction using the R package MutationalPatterns. A mutational process was deemed active in a sample if >150 SNVs and >10% of SNVs in a cluster were attributed to a mutational process by de novo signature extraction. The majority of ALL patients with multiple relapses had a mutational load above average, compared to an unselected diagnosis cohort, which often increased during disease progression. Six cases (21%) passed the hypermutation threshold of 1.3 mutations/Mb as previously defined (Waanders et al., 2020). However, mutational signature analysis revealed that mutational processes were active in a much larger proportion of cases. We extracted 7 single base substitution (SBS) signatures, of which 4 were known COSMIC signatures (cosine similarity >0.95) and 2 were similar to known COSMIC signatures (cosine similarity >0.8). At time of diagnosis 4 distinct mutational processes were found to be active alone or in combination in 10 cases (36%), which is much higher than an unselected diagnosis cohort (13%). These processes included APOBEC-associated mutagenesis (SBS2 & SBS13), a mutational pattern resembling UV-like damage (SBS7a), a process that may be caused by reactive oxygen species (SBS18-like) and an unknown process (Fig. 1). By clustering SNVs per patient in time we followed the activity of mutational processes and identified rising and falling (sub)clones. APOBEC mutagenesis was found to be an ongoing process, sometimes appearing for the first time at relapse (Fig. 1B), although when xenografted in mice (n=2) no continued mutagenesis was observed. SBS7a or SBS18-like mutagenesis always occurred already at diagnosis. One patient, who relapsed 5 times, acquired at each presentation between 500-1500 new SNVs with a specific pattern that did not match any known cosmic mutational signatures, and may represent a novel intrinsic mutational mechanism. At time of relapse, additional (mostly treatment-related) mutational processes became active, eventually affecting 17/28 (61%) patients (Fig. 1A), much higher than observed in cases with single relapses (~40%; Li et al., 2020, Blood, 135:41). We observed the thiopurine-associated SBS87 in 9 (32%) patients, and an unexplained SBS86-like mutational signature in 2 patients (Fig. 1B). Furthermore, we noticed SBS17-like mutagenesis in one patient. The etiology of SBS17 is as yet not established, but it has been proposed to be caused by reactive oxygen species. To conclude, ALL patients with multiple relapses showed an increased prevalence and large variety of interplaying mutational processes at diagnosis (36%) and final relapse (61%), with intrinsic or therapy induced origins. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Genomic Panorama and Clonal Evolutionary Trajectory of Classical Hairy Cell Leukemia

Classical Hairy Cell Leukemia (HCLc) is a rare B-cell malignancy characterized by hairy-like cell membrane projections. The cell of origin and pathway of malignant transformation in HCLc remain unknown. Early work using whole exome sequencing identified BRAFV600E as a genetic hallmark in HCLc (Tiacci et al 2011 and Weston-Bell et al 2016). However, no other recurrent coding mutations appeared, marking it an uncommon monogenic cancer. As BRAFV600E appears insufficient to drive tumorigenesis in other cancers (Dankort et al 2009; Rad et al 2013), it suggested that other driver alterations may be implicated in HCLc pathogenesis, perhaps in the non-coding genome, overlooked in exome studies alone. To probe this, we carried out whole genome sequencing (WGS) in HCLc. We established the genomic panorama, and importantly leveraged data to derive tumor phylogenies to determine the relative order of early driver mutational events that associate with the most recent common ancestor (MRCA) of all tumor cells. WGS was performed in 10 typical HCLc cases each paired with germline in purified cell sorted populations of disaggregated splenocytes. Sequencing involved 150 bp paired ends on Illumina HiSeq4000. Data analyses included identification of somatic single-nucleotide variants (SNVs) and small indels using CaVEMan and Pindel, respectively; copy-number aberrations (CNA) with Battenberg; and structural variants (SVs) with BRASS. The fitting of COSMIC mutational signatures was performed using mmsig. Mutational SNVs and CNA drivers were used for the analysis of tumor phylogenesis of individual tumors. We mapped the whole genome landscape in HCLc. Somatic coding variants emerged as previously reported. BRAFV600E was present as a clonal mutation in all HCLc tumors. Missense mutations in KLF2 (p.S275N and p.S275I) were identified in 2 tumors. Two somatic SNVs were detected in PRSS3 (p.D95G and p.R94S) and ANKRD30B (p.K388E and p.N392K) in 2 different cases respectively. In the noncoding genome, BCL6 and ZFP36L1 promoters were recurrently mutated in 5/10 cases. Driver mutations in BCL6 promoters have been reported in other B-cell malignancies to disrupt negative autoregulatory circuits (Pasqualucci et al 2003). Analysis of CNA showed a relatively stable genome (ploidy ~2). A large CNA chr5 gain was observed in a single tumor. Two additional focal CNA were spotlighted at chr17q25 (Gain) and chr20q11 (LOH) in two individual tumors. A recurrent interchromosomal translocation at chr12q14.3 locus was identified in 5 individual tumors, and an identical translocation at 14q21.3 with 15q11.2 observed in 2 tumors. Interestingly, novel kataegis-like mutations were observed at TRB loci across all HCLc cohort samples. We further identified somatic hypermutation (SHM) imprints in non-Ig loci, notably in BCL6. The mutational rate of AID targets at TRB and non-Ig loci were comparable to SHM occurring in Ig IGV genes. Deciphering the mutational signatures in HCLc genomes highlighted SBS9, a mutational signature associated with SHM in B-cell leukemia as one of the most relevant mechanisms, allied to the clock-like signatures of SBS1 and SBS5. Next, we utilized estimates of the cancer cell fraction to define which mutations are clonal and associate with the MRCA, and which mutations occured subclonally to derive individual tumor phylogenetic trees using methodology we have reported previously (Rabbie et al 2020; Ansari-Pour 2021). Here, analyses of clonal trajectories revealed that BRAFV600E occurred prior to subclonal diversification in MRCA in all cases. Significantly however, 1 or 2 additional driver mutations were conjointly detected with BRAFV600E in the MRCA in 6/10 HCLc cases prior to any subclonal evolution. Our data provide a comprehensive map of the whole genome in HCLc for the first time. Clonal evolutionary trajectories reveal heterogeneous genetic origins in HCLc, in which BRAFV600E is the sole driver mutation in one subset of disease, but requires 1 or 2 additional mutational drivers in the other subset to promote malignant transformation. Thus, unlike other cancers, BRAFV600E alone appears to suffice to induce malignant transformation in some HCLc. Additionally, SHM in non-Ig loci including BCL6 may implicate early traffic of the tumor cell of origin through the germinal center and early exit prior to acquisition of CD27, or mutational events at ectopic sites.

Deciphering the Somatic and Germline Structural Variation Landscape in Pediatric B-Cell Precursor Acute Lymphoblastic Leukemia By Whole Genome Optical Mapping

Background: B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is the most frequent pediatric cancer. The most common numerical and structural chromosomal alterations are high hyperdiploidy (HHD, 51-67 chromosomes) and t(12;21)(p13;q22) leading to ETV6::RUNX1 fusion. However, for a full-blown leukemia, secondary alterations are required. Furthermore, it is increasingly recognized that germline variants may enhance ALL susceptibility in ~4% of the patients (Bloom et al. 2019, Klco & Mullighan 2020). In large-scale genomic studies, the mutational landscape of somatic and germline single nucleotide variants and small indels has been well described in BCP-ALL. However, a comprehensive analysis of somatic and germline structural variants (SVs) in ETV6::RUNX1 and HHD tumors is still lacking. Recent feasibility studies showed that whole genome optical mapping (WGOM) is a novel method for reliable SV detection which could abrogate conventional cytogenetics and array based methods in the future (Neveling et al. 2021, Mantere et al. 2021). The aim of the study was to analyze the structural variation landscape in pediatric BCP-ALL patients by employing WGOM to gain significant insights on leukemia predisposition and development. Methods: We studied 60 pediatric patients diagnosed with ETV6::RUNX1 (n=30) or HHD (n=30) BCP-ALL with a median age at diagnosis of 3.9 (range 1.7-17) and a male to female ratio of 1.14:1. We collected tumor material at initial diagnosis and included fibroblast or remission material as matched non-tumor control of each patient. Ultra-high molecular weight DNA was extracted from 120 samples and labeled by a sequence specific enzyme. Fluorescently labeled DNA was analyzed using a Saphyr instrument (Bionano Genomics). We integrated comprehensive datasets of 60 matched tumor/non-tumor genomes to identify somatically acquired SVs >500bp. Corresponding data of standard methods as cyto- (karyotype, fluorescence in situ hybridization) and molecular genetics (SNP-array) of the leukemia samples were compared to WGOM data. In addition, the prevalence of rare germline SVs (<1% of 160 healthy control samples [Bionano] and minor allele frequency <0.01 in dbVar) occurring in known cancer predisposition genes was analyzed in the non-tumor samples. Results: WGOM was able to detect 94% (438/464) of previously observed events by conventional methods, including ETV6::RUNX1 and high hyperdiploid hallmark alterations in all BCP-ALL cases. Beyond that, we discovered 895 additional SVs with WGOM not detected by standard cyto- and molecular genetics. WGOM detected a median of 25 (range 0-70) somatic SVs secondary to the hallmark alterations in ETV6::RUNX1 tumors compared to 13 (range 0-28) SVs in HHD cases. We identified 60 recurrently altered regions occurring in ≥3 BCP-ALL cases including 12p13.2 (ETV6, 19/60), 9p13.2 (PAX5, 13/60), 9p21.3 (CDKN2A/B, 12/60), 11p12 (RAG2, 10/60), 20p12.2 (MKKS/SLXIP, 10/60) or 3q13.2 (CD200/BTLA, 8/60). We detected ETV6::RUNX1 subtype specific recurrent focal deletions in ATF7IP (10/30), BTG1 (10/30), NSD2 (5/30) and TBL1XR1 (4/30). Interestingly, we discovered recurrent SVs affecting putative novel genes involved in BCP-ALL leukemogenesis such as STAG2, GPN3 and UBA2 which are affected in ~10% of the BCP-ALL patients. Strikingly, WGOM revealed in total 9 novel potential in-frame fusion transcripts in both tumor subtypes, including a potential fusion of the cohesin complex members PDS5B::STAG2, arising through a t(X;13)(q25;q13.1) in an ETV6::RUNX1 patient (Figure 1). In addition, we detected 28 rare germline SVs targeting 22 known cancer predisposing genes in 35% (21/60) of the pediatric patients. 40% (9/22) of the affected genes were involved in hematopoietic or lymphoid organ development as ETV6, FANCA, IKZF1, ITCH or PTPRC. In 18% (11/60) of the children, the identified germline alteration potentially altered a coding region of a known cancer predisposing gene including a duplication of CIITA in an ETV6::RUNX1 patient. Conclusions: By applying the novel technology WGOM, we could detect a significant amount of previously hidden SVs in our BCP-ALL cohort in addition to conventional methods. We further generated a comprehensive landscape of somatic and germline SVs in childhood BCP-ALL, revealing recurrently altered regions and novel potential players in ALL leukemogenesis and predisposition. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Clonal Evolution of Cutaneous T Cell Lymphoma Revealed at Single Cell Resolution

Background: Patients with Cutaneous T Cell Lymphoma (CTCL) subtypes Mycosis Fungoides and Sézary Syndrome (MF/SS) who progress to advanced stage disease have a 20% 5-year overall survival rate. Current treatments for CTCL range from localized therapies for skin lesions to systemic treatments, including histone deacetylase inhibitors, chemotherapy, and immunotherapy. While many treatments are initially effective, patients often develop resistance to ongoing treatment. Though recent studies have comprehensively profiled the genomic landscape of CTCL, no clear driver mutation has been identified and the molecular factors that drive MF/SS progression remain undefined. To address these outstanding questions, we collected longitudinal tumor and normal samples from 10 MF/SS patients and subjected them to high resolution genome and transcriptome analyses (exome, whole genome and single-cell RNA sequencing, eWGS and scRNAseq) to define the clonal evolution and temporal progression of CTCL. Methods: We collected 52 serial tumor samples (peripheral blood, skin and lymph node biopsies, 49-1050 days apart) and matched, purified non-malignant cells from 10 MF/SS patients (3 - 8 specimens per patient) representative of patients seen at the Washington University School of Medicine Cutaneous Lymphoma clinic (mean age 56.1 years, 50% female, 60% Caucasian and 40% African American). All were diagnosed with advanced MF and/or SS and half of first specimens were collected within 60 days of diagnosis. Subsequent specimens were collected at progression or lack of response to therapy, on average 20 months between specimens (1.4 - 60, SD = 11.8); patients had received 1-11 different CTCL therapies. For eWGS, specimens were purified by flow cytometry as follows, tumor: CD3+CD4+CD7- and normal: CD4+CD7+ (non-malignant T cells) or CD3-CD14+ (monocytes) or CD3-CD56+ (NK cells). Specimens were subjected to scRNAseq, exome sequencing plus low coverage whole genome sequencing (eWGS), and patient specific TCR clonotype assignment (scRepertoire). Results: Clustering and cell type inference of scRNAseq (UMAP/Seurat/singleR) from 92,496 total cells showed canonical CTCL marker genes and high clonal proportions (1-100%) of patient specific TCR clonotypes. Somatic genome copy number variants (CNV) from eWGS (cnvkit) and scRNAseq (copykat) and deleterious/damaging single nucleotide variants (SNV) (eWGS, GATK/Mutect2; scRNAseq, cb_sniffer) were identified in CTCL versus matched, non-malignant cells. To segregate early genomic events from those that were progression-associated, we developed an integrative analysis pipeline to prioritize somatic CNV and SNV that were detected in samples collected at timepoints with lack of response to therapy and/or progression in ≥30% of patients. This novel approach revealed alterations in T-cell activation pathways as early events that were maintained in subsequent CTCL samples. Loss of some chromatin-modifying enzymes were early events, while gains of others (DNMT3A, EZH2, KMT2C) were acquired with therapy resistance/progression (Fig. 1A). Copy number amplifications of STAT3/STAT5 are frequent and we demonstrate a novel-to-CTCL single nucleotide mutation in STAT3 that has gain-of-function activity. Progression-associated genomic changes were enriched in cell cycle (CDK genes), DNA damage/repair (TP53BP1, RAD51C), RAS and Rho signaling pathways, and transcriptional regulators (FOXO genes). Expression of mutant alleles was detectable in scRNAseq and variant levels fluctuated with progression or lack of therapy response (Fig. 1B). Conclusion: To date, there have been limited studies defining temporal changes in the genomes and transcriptomes of CTCL due in part to low tumor burden in the skin and blood. Using innovative sequencing and informatic approaches, we identified recurrent alterations in CDK11A, DNMT3A, EZH2, FOXO1, RAD51C, STAT3/STAT5, and TP53BP1, among others, with clonal evolution in CTCL. Many of these have therapeutic implications. Taken together, these findings represent new insights into MF/SS progression, reveal new markers for response assessment, and identify new targets for therapeutic development. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Replacing Procarbazine with Dacarbazine in Escalated Beacopp Dramatically Reduces the Post Treatment Haematopoietic Stem and Progenitor Cell Mutational Burden in Hodgkin Lymphoma Patients with No Apparent Loss of Clinical Efficacy

Introduction When treating Hodgkin lymphoma (HL), it is common UK practice to modify escalated BEACOPP (eBPP) by removing oral procarbazine and replacing it with intravenous dacarbazine (250mg/m2 D2-3) to reduce haematopoietic stem cell and gonadal toxicity. A similar replacement of procarbazine in COPP (to COPDac) has reduced gonadal toxicity and conferred a comparable long-term event-free survival to children (EuroNet-PHL-C1 trial; Mauz-Körholz et al Lancet Oncol 2021). Our own retrospective study has shown that adults treated with first-line escalated BEACOPDac (eBPDac) have a reduced blood transfusion requirement and earlier return of menstrual periods compared with real-world eBPP patients (pts) with no loss of clinical efficacy compared to HD18 eBPP pts (Santarsieri et al Blood 2021). To better understand the toxicity differences, we performed this study to compare the haematopoietic stem and progenitor cell (HSPC) mutational burden in pts who have received procarbazine and dacarbazine containing regimens. Chemotherapeutic agents are known to damage DNA and this mutational process likely causes many of the long-term chemotherapy toxicities. Little is known about the mutational signatures and mutation burdens caused by HL therapies, although a novel mutational signature (SBS25) has recently been described in two HL cell lines (Petljak et al Cell 2019). Methods We whole genome sequenced 6-8 single-cell derived HSPC colonies from each of 12 advanced stage HL pts (n = 91; mean sequencing depth 26X). The pts were all in remission > 6 months and had been previously treated with either eBPDac (6 cycles (n=2); 4 cycles (n=2)), eBPP (6 cycles (n=3); 5 cycles (n=1); 4 cycles (n=1)) or ABVD (n=3; all 6 cycles). Single HSPC somatic mutation burdens and mutation spectra from these chemotherapy exposed individuals were compared to those from our previously published normal cohort (n = 110; mean sequencing depth 24X) (Mitchell et al Nature 2022). In addition we have updated the outcomes of our retrospective multi-centre study of pts treated with eBPDac including additional pts and longer follow-up of the entire cohort. Mutational analysis The somatic single nucleotide variant mutation burden in normal adult HSPCs ranges from approximately 400 aged 20yr to 1500 aged 80yr; an average of 18 mutations accumulate with every year (Figure 1A). The HSPCs from ABVD and eBPDac-treated pts had similar minor excess somatic mutation burdens compared to aged-matched normal HSPCs of 183 (CI95%= 110-256) and 291 (CI95%= 242-340) mutations respectively. In contrast, the HSPCs from eBPP-treated pts had a striking and significantly increased excess mutation burden of 1153 (CI95%= 937-1369). Of the eBPP pts, the single patient who received 4 cycles had the lowest number of excess mutations, but noting the inter-patient variation, we cannot yet conclude that eBPP cycle number correlates with the number of mutations. Descriptive analysis of the mutational profiles (Figure 1B) revealed that every patient who received procarbazine had a clear SBS25-like mutational signature, characterised by T>A base substitutions, demonstrating for the first time that this DNA mutational signature is directly attributable to procarbazine. Clinical data analysis The clinical data presented last year have been updated with more pts and longer follow-up (n=288; median 2.3 yr). With this high-risk group of advanced stage pts, our data suggest that the eBPDac pts have reduced red cell transfusion requirements, reduced hospitalisation, improved menstrual period recovery and improved sperm count preservation compared with eBPP pts. The eBPDac 24-month PFS is similar to HD18 3-yr PFS (94.9% vs 92.3%) and appears superior to RATHL 5-yr PFS (81.4%). The eBPDac 24-month OS estimate is 99%. Conclusions We have shown that dacarbazine-containing regimens (ABVD and eBPDac) confer a lower mutation burden to HSPCs compared with procarbazine-containing eBPP and that procarbazine is the agent responsible for the SBS25 mutational signature. This work provides a model example of how genomic analysis could be used to inform therapeutic decision making in cancer. Our retrospective analysis provides strong supportive evidence that eBPDac is a highly efficacious HL treatment and noting the clear benefits in terms of HSPC genomic health, we would encourage clinicians offering eBPP to HL pts to consider replacing procarbazine with dacarbazine. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Genotyping and Minimal Residual Disease (MRD) Assessment in cfDNA By the Euroclonality-NGS DNA Capture (EC-NDC) Panel in Mantle Cell Lymphoma (MCL)

Background Modern concepts for the treatment of mantle cell lymphomas (MCL) increasingly integrate clinical and biological variables for risk-adapted treatment strategies. Novel next-generation sequencing (NGS) technologies are highly suited for tumor genotyping as well as disease monitoring by minimal residual disease (MRD) assessment, identifying patients (pts) with a high risk of relapse. Here, we investigated whether the EuroClonality (EC)-NGS DNA Capture (EC-NDC) assay is a) applicable for genotyping of MCL in peripheral blood (PB) and plasma cell-free (cf)DNA and b) suitable for MRD assessment in plasma as compared to the amplicon-based EuroClonality Immunoglobulin-based (IG-)NGS assay. Patients and methods A total of 109 PB samples (55 baseline and 54 interim staging) from a cohort of MCL treated within the TRIANGLE trial by the European MCL network (NCT02858258) were selected according to a PB infiltration ≥10% at diagnosis. From prospectively collected PB samples in national reference labs, DNA from the cellular blood compartment (PBC) and plasma cfDNA was extracted. For targeted capture, the EC-NDC assay (Univ8® Genomics, UK) was used to simultaneously detect immunoglobulin and T cell receptor (IG/TR) rearrangements, structural variants (SV) and single nucleotide variants (SNVs) in 72 genes (Stewart, Blood Adv, 2021). For diagnostic PBC and cfDNA samples, IG clonotypes were called with ≥6 unique reads and ≥5% of annotated IG reads, SV were called with ≥4 unique reads and SNV were called with ≥6 unique reads at ≥4% variant allele frequency (VAF). For amplicon-based MRD analysis the EuroClonality IG-NGS (IG-NGS) assay was used with IG clonotypes called with ≥5% of annotated IG reads and at ≥1 log higher abundance to the polyclonal background. MRD was analyzed by IG-NGS in PBC using 8 µg PBC DNA to reach a sensitivity of 10-6. For MRD analysis in cfDNA, we aimed to use ≥5000 genome equivalents (GE) for both IG-NGS and EC-NDC. Data were analyzed by ARResT/Interrogate (Bystry, Bioinformatics, 2017) with an adapted pipeline for targeted capture in cfDNA. MRD status was defined as positive by detecting a lymphoma-specific IG clonotype and/or SV at ≥1 read, or alternatively by retrieval of ≥1 disease-specific mutation at ≥3 reads. Results Total cfDNA amounts at baseline were high (mean 92.6 ng/mL plasma) and even increasing at interim staging (mean 123.8 ng/mL) while decreasing by 10-fold in 38 samples at end of treatment (EoT)(mean 11.45 ng/mL). At baseline, a tumor-specific IGH-VJ clonotype was detected by IG-NGS in all 55 PBC and cfDNA samples. Genotyping by EC-NDC showed fully concordant results in 55 PBC and cfDNA samples with respect to IG clonotypes, SV and SNV, except for 3 PBC samples with low usable reads covering IGH-VJ regions. The presence of a t(11;14)(q13;q32) translocation was confirmed in 54/55 pts in PBC and cfDNA, while one patient with unknown t(11;14) translocation status by FISH was negative by EC-NDC. EC-NDC identified 106 putative somatic SNVs (VAF 2.7-75%, median 30%) in PBC and cfDNA, and among those were genes described as drivers in MCL (ATM (25/55), TP53 (11/55), KMT2D (9/55), SAMHD1 (5/55), CCND1 (5/55) and 18 other genes (Fig. 1). Six pts with detectable t(11;14) and IG rearrangement did not show additional SNVs. On average, 6 MRD markers/pt were identified (range: 3-10). At interim staging, MRD was analyzed in 54 PBC and 44 cfDNA samples. Twenty-five (47%) pts were MRD+ in PBC by IG-NGS. Twenty (46%) pts were MRD+ in cfDNA by EC-NDC (8 cases with ≥2 markers, 4 with 2 markers, and 8 with 1 marker). From 10/44 (23%) cfDNA samples MRD+ by IG-NGS, 9 were also MRD+ by ED-NDC. From 44 pts with parallel analysis of PBC and cfDNA, 14 (32%) were MRD+ and 18 (41%) were MRD-, while 12 (27%) showed discordant results. Conclusion To the best of our knowledge, this is the first analysis comparing targeted capture and amplicon assays for application in PBC and cfDNA in MCL. The capture-based EC-NDC assay allows a comprehensive liquid biopsy-based genotyping of MCL. In addition, both IG-NGS and EC-NDC assays are suitable for MRD assessment in cfDNA with evidence of more sensitive MRD detection EC-NDC due to multiple MRD targets detected and traced by this assay. Clinical data are still needed to explore the potential prognostic impact of MRD assessment in plasma vs PBC. Updated MRD analysis at EoT and correlation with clinical data will be presented at the meeting. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Analytical and clinical validation of a custom 15-gene next-generation sequencing panel for the evaluation of circulating tumor DNA mutations in patients with advanced non-small-cell lung cancer.

BackgroundThis is a pilot proof-of-concept study to evaluate the utility of a custom 15-gene circulating tumor DNA (ctDNA) panel as a potential companion molecular next-generation sequencing (NGS) assay for identifying somatic single nucleotide variants and indels in non-small-cell lung cancer (NSCLC) patients. The custom panel covers the hotspot mutations in EGFR, KRAS, NRAS, BRAF, PIK3CA, ERBB2, MET, KIT, PDGFRA, ALK, ROS1, RET, NTRK1, NTRK2 and NTRK3 genes which serve as biomarkers for guiding treatment decisions in NSCLC patients.MethodThe custom 15-gene ctDNA NGS panel was designed using ArcherDX Assay Designer. A total of 20 ng or 50 ng input ctDNA was used to construct the libraries. The analytical performance was evaluated using reference standards at different allellic frequencies (0.1%, 1%, 5% and parental). The clinical performance was evaluated using plasma samples collected from 10 treatment naïve advanced stage III or IV NSCLC patients who were tested for tissue EGFR mutations. The bioinformatics analysis was performed using the proprietary Archer Analysis Software.ResultsFor the analytical validation, we achieved 100% sensitivity and specificity for the detection of known mutations in the reference standards. The limit of detection was 1% allelic frequency. Clinical validation showed that the clinical sensitivity and specificity of the assay for detecting EGFR mutation were 83.3% and 100% respectively. In addition, the NGS panel also detected other mutations of uncertain significance in 6 out of 10 patients.ConclusionThis preliminary analysis showed that the custom 15-gene ctDNA NGS panel demonstrated good analytical and clinical performances for the EGFR mutation. Further studies incorporating the validation of other candidate gene mutations are warranted.