Germline Whole Exome Sequencing Research Articles

A method to comprehensively identify germline SNVs, INDELs and CNVs from whole exome sequencing data of BRCA1/2 negative breast cancer patients.

In the rapidly evolving field of genomics, understanding the genetic basis of complex diseases like breast cancer, particularly its familial/hereditary forms, is crucial. Current methods often examine genomic variants-such as Single Nucleotide Variants (SNVs), insertions/deletions (Indels), and Copy Number Variations (CNVs)-separately, lacking an integrated approach. Here, we introduced a robust, flexible methodology for a comprehensive variants' analysis using Whole Exome Sequencing (WES) data. Our approach uniquely combines meticulous validation with an effective variant filtering strategy. By reanalyzing two germline WES datasets from BRCA1/2 negative breast cancer patients, we demonstrated our tool's efficiency and adaptability, uncovering both known and novel variants. This contributed new insights for potential diagnostic, preventive, and therapeutic strategies. Our method stands out for its comprehensive inclusion of key genomic variants in a unified analysis, and its practical resolution of technical challenges, offering a pioneering solution in genomic research. This tool presents a breakthrough in providing detailed insights into the genetic alterations in genomes, with significant implications for understanding and managing hereditary breast cancer.

Feasibility and Clinical Utility of Reporting Hereditary Cancer Predisposition Pathogenic Variants Identified in Research Germline Sequencing: A Prospective Interventional Study.

Patients with cancer frequently undergo research-grade germline sequencing but clinically actionable results are not routinely disclosed. The objective of this study is to evaluate the feasibility of reporting clinically relevant secondary findings (SF) identified in germline research sequencing using the institutional molecular tumor board (MTB) and the treating oncology physician. This prospective, interventional cohort study enrolled Total Cancer Care participants with any cancer diagnosis at a single institution. Patients underwent research-grade germline whole-exome sequencing, with bioinformatic analysis in a Clinical Laboratory Improvement Amendments-certified laboratory to verify pathogenic/likely pathogenic germline variants (PGVs) in any American College of Medical Genomics and Genetics SF v2.0 genes. After a protocol modification in consenting patients, the MTB reported PGVs to treating oncology physicians with recommendations for referral to a licensed genetic counselor and clinical confirmatory testing. Of the 781 enrolled participants, 32 (4.1%) harbored cancer predisposition PGVs, 24 (3.1%) were heterozygous carriers of an autosomal recessive cancer predisposition syndrome, and 14 (1.8%) had other hereditary disease PGVs. Guideline-directed testing would have missed 37.5% (12/32) of the inherited cancer predisposition PGVs, which included BRCA1, BRCA2, MSH6, SDHAF2, SDHB, and TP53 variants. Three hundred fifteen participants consented to reporting results; results for all living patients were reported to the clinical team with half referred to a licensed genetic counselor. There was concordance between all research variants identified in patients (n = 9) who underwent clinical confirmatory sequencing. MTB reporting of research-grade germline sequencing to the clinical oncology team is feasible. Over a third of PGVs identified using a universal testing strategy would have been missed by guideline-based approach, suggesting a role for expanding germline testing.

Germline whole-exome sequencing of patients with neuroendocrine neoplasms (NENs) reveals pathogenic or likely pathogenic variants in a large subset of patients

Germline whole-exome sequencing of patients with neuroendocrine neoplasms (NENs) reveals pathogenic or likely pathogenic variants in a large subset of patients

Confirmed Pathogenic Germline Variants in Cancer Predisposition Genes Incidentally Detected in Somatic Genomic Profiling of Multiple Myeloma Patients

Introduction: We previously showed that ~10% of patients with multiple myeloma (MM) carry pathogenic or likely-pathogenic (P/LP) germline variants (PGVs) in known cancer predisposition genes, and that moderate/high-penetrance PGVs in DNA repair genes may be associated with MM risk and favorable response to alkylating chemotherapy. Increasingly applied in MM, genomic profiling by next-generation sequencing (NGS) can identify prognostically-relevant and therapeutically-actionable somatic mutations, but it may also incidentally unveil PGVs, which can have significant implications for patients and their families. We here test the diagnostic accuracy of a novel referral tool designed to flag likely PGVs warranting confirmatory germline testing among mutations identified in somatic NGS studies of 1161 MM patients from our institution. Methods: We retrospectively reviewed 1715 commercial NGS reports of 1161 MM patients treated at the Icahn School of Medicine at Mount Sinai (ISMMS) between 2015 & 2022 (targeted 448-gene somatic profiling panels performed by a single genomic testing company for clinical purposes on bone marrow aspirate samples). In collaboration with certified genetic counselors at our institution, we applied evidence-based criteria to develop a tool to flag P/LP variants of likely germline origin warranting a referral for confirmatory germline testing (“Likely PGVs”). The resulting referral tool flags variants detected in 35 well-established cancer predisposition genes at a variant allele frequency (VAF) of >10%, as well as 24 cancer predisposition founder variants at any VAF. Next, we tested the positive predictive value (PPV), negative predictive value (NPV), sensitivity and specificity of our approach for the detection of true PGVs by analyzing paired germline whole-exome sequencing (WES) in 382/1161 (33%) MM patients in the study cohort. Germline WES data were generated for research purposes using a clinically-validated pipeline for PGV detection and annotation. Results: 385 P/LP variants were reported in somatic NGS studies of 382 MM patients who had paired somatic/germline sequencing data. Of these, 38/385 (9.9%) were found to be true PGVs in confirmatory germline testing. True PGVs detected in more than one gene included nine APC, seven CHEK2, five BRCA1, three BRCA2, three ATM and three MUTYH variants. The referral tool flagged 41/385 (10.6%) of the cohort's somatic variants as likely PGVs, identifying 32/38 (84.2%) true PGVs. The six PGVs missed by the referral tool were detected in the following genes: one APC, one CHEK2, one MITF, one MUTYH, one NF1 and one SHDA variant. In contrast, the nine variants that were mislabeled as likely PGVs but were in fact somatic were: two ATM, two BRCA2, two TSC1, one CHEK2, one BRIP1, and one RET. With a variant allele threshold of >10%, the tool had a PPV of 78.0% and a NPV of 98.3% for the detection of true PGVs. The sensitivity and specificity were 84.2% and 97.5%, respectively. Among the 692/1161 MM patients who did not have confirmatory germline testing (67%), the proportion of variants flagged as likely PGVs was very similar to that of the paired somatic/germline group (77/696, 11.1%), and variants were detected in similar genes. Assuming a PPV of 78%, 60 of these variants could represent true PGVs. Conclusion: A novel tool designed to flag likely PGVs among mutations identified in somatic genomic profiling of MM patients had high sensitivity and specificity for the detection of true PGVs. 9.9% of all MM patients with paired somatic/germline testing were found to have a true PGV, validating the results of our prior study and once again highlighting the need to implement screening strategies in high-risk subgroups of MM patients, such as those with strong family history of cancer or prior personal history of cancer.

The mutational landscape of skull base and spinal chordomas and the identification of potential prognostic and theranostic biomarkers.

Chordomas are rare bone neoplasms characterized by a high recurrence rate and no benefit from any approved medical treatment to date. However, the investigation of molecular alterations in chordomas could be essential to prognosticate, guide clinical decision-making, and identify theranostic biomarkers. The aim of this study was to provide a detailed genomic landscape of a homogeneous series of 64 chordoma samples, revealing driver events, theranostic markers, and outcome-related genomic features. The authors conducted whole-exome sequencing (WES), targeted next-generation sequencing, and RNA sequencing of 64 skull base and spinal chordoma samples collected between December 2006 and September 2020. Clinical, histological, and radiological data were retrospectively analyzed and correlated to genetic findings. The authors identified homozygous deletions of CDKN2A/2B, PIK3CA mutations, and alterations affecting genes of SWI/SNF chromatin remodeling complexes (PBRM1 and ARID1A) as potential theranostic biomarkers. Using matched germline WES, they observed a higher frequency of a common genetic variant (rs2305089; p.(Gly177Asp)) in TBXT (97.8%, p < 0.001) compared to its distribution in the general population. PIK3CA mutation was identified as an independent biomarker of short progression-free survival (HR 10.68, p = 0.0008). Loss of CDKN2A/2B was more frequently observed in spinal tumors and recurrent tumors. In the current study, the authors identified driver events such as PBRM1 and PIK3CA mutations, TBXT alterations, or homozygous deletions of CDKN2A/2B, which could, for some, be considered potential theranostic markers and could allow for identifying novel therapeutic approaches. With the aim of a future biomolecular prognostication classification, alterations affecting PIK3CA and CDKN2A/2B could be considered as poor prognostic biomarkers.

Whole exome germline sequencing in early-onset prostate cancer patients: Genomic findings and clinical outcomes.

Whole exome sequencing (WES) furthered our understanding of various tumors. We assessed the occurrence of germline likely pathogenic/pathogenic (LP/P) variants, disease features, and clinical outcomes in early-onset prostate cancer. This retrospective study (N = 134) included consecutive prostate cancer patients who donated blood samples for research purposes to the Kahn-Sagol-Maccabi biobank. Patients diagnosed at >65 years were excluded. Clinical characteristics were extracted from the medical records. Germline WES was performed with analysis reporting on oncogenetic, two immunogenic, and a secondary minimum list panels (121, 468, 76, and 59 genes, respectively). Median age at diagnosis was 61 (range 46-65) years; 131 (98%) were diagnosed with local disease. The median follow-up time from diagnosis was 14 (range <1-25) years. Of the patients with local disease, 32 (24%) and 10 (8%) had biochemical and distant recurrences, respectively. Twenty-five patients (19%) had ≥1 additional cancer (excluding non-melanoma skin cancer), most frequently bladder (6), colorectal (5), and lymphoma (5). Seven (5%) deaths were reported, with only one related to prostate cancer. LP/P variants were identified in 8 patients (6%), all in genes from the oncogenetic panel: ATM, BRCA1 (in two patients), BRCA2 (in two patients), HOXB13, MUTYH, and MYH7. Of these eight patients, with a median follow-up of 7 years (range <1-15), two (25%) had biochemical recurrences, one had (12.5%) distant recurrence, and no deaths were reported. In this cohort of 134 early-onset prostate cancer patients, we identified germline LP/P variants in an oncogenetic panel in 6% of participants, with no unique clinical outcome.

Predicting Cancer Risk from Germline Whole-exome Sequencing Data Using a Novel Context-based Variant Aggregation Approach.

There is evidence that cancer is partly caused by rare genetic variants that have not yet been identified. We investigate this issue using novel statistical methods and data from the UK Biobank.

Inherited cancer predisposing mutations in patients with therapy-related myeloid neoplasms.

Some patients with therapy-related myeloid neoplasms (t-MN) may have unsuspected inherited cancer predisposition syndrome (CPS). We propose a set of clinical criteria to identify t-MN patients with high risk of CPS (HR-CPS). Among 225 t-MN patients with an antecedent non-myeloid malignancy, our clinical criteria identified 52 (23%) HR-CPS patients. Germline whole-exome sequencing identified pathogenic or likely pathogenic variants in 10 of 27 HR-CPS patients compared to 0 of 9 low-risk CPS patients (37% vs. 0%, p=0.04). These simple clinical criteria identify t-MN patients most likely to benefit from genetic testing for inherited CPS.

A germline exome analysis reveals harmful POT1 variants in multiple myeloma patients and families.

Observations of inherited susceptibility to multiple myeloma have led to active research in defining predisposing genes to the disease. Here, we analysed 128 plasma cell dyscrasia patients' germline whole-exome sequencing data. Rare dominantly inherited pathogenic or likely pathogenic (P/LP) variant was found in 9.4% of the patients. Among the P/LP variants, CHEK2 (p. Thr410MetfsTer15) was the most prevalent (n= 5, 3.9%). Interestingly, P/LP variants in POT1 wereidentifiedinthree patients(2.3%). Our findings broaden the spectrum ofPOT1-relatedcancers and demonstrate the importance of the germline genetic analysis in hematological malignancies.

Whole-Exome Sequencing Identifies Pathogenic Germline Variants in Patients with Lynch-Like Syndrome.

Simple SummaryA significant proportion of families with a clinical suggestion of Lynch syndrome and screened for the known MMR genes remain without a molecular diagnosis. These patients, who generally show a suggestive family pedigree or early-onset tumors with MMR deficiency and no detectable germline variants, are referred to as having Lynch-like syndrome. To investigate underlying and potentially predisposing variants related to Lynch-like syndrome, we performed whole-exome sequencing in patients with clinical criteria for Lynch syndrome, MMR deficiency and without germline variants. This approach allowed for the identification of new variants potentially associated with Lynch-like syndrome, providing new clues to explain the familial predisposition to Lynch syndrome-related tumors in these patients, which could lead to new screening strategies for the identification of families at risk of developing cancer.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 sequencing (WES). A total of 20 unrelated patients with MMR deficiency who met the clinical criteria for LS and had no germline variant were subjected to germline WES. Variant classification was performed according to the American College of Medical Genetics and Genomics (ACMG) criteria. Pathogenic/likely pathogenic variants were identified in 35% of patients in known cancer genes such as MUTYH and ATM. Besides this, rare and potentially pathogenic variants were identified in the DNA repair gene POLN and other cancer-related genes such as PPARG, CTC1, DCC and ALPK1. Our study demonstrates the germline mutational status of LLS patients, a population at high risk of colorectal cancer.

Abstract 1151: Pharmacogenomics genotyping from clinical somatic whole exome sequencing: Aldy, a computational tool

Abstract Background Pharmacogenomics (PGx) testing can reduce toxicities and improve efficacy of several drugs used to treat cancer and associated symptoms. PGx results can be determined from germline whole-exome sequencing (WES), but somatic mutations may cause discordance between tumor and germline DNA. Since clinical diagnostic sequencing in oncology frequently only includes tumor DNA, there would be clinical value in calling germline PGx genotypes from tumor DNA. Thus, the purpose of this study was to assess the feasibility of using somatic WES data to call germline PGx genotypes. Methods Germline and somatic WES data were obtained as part of the clinical workflow for 64 patients treated at the solid molecular tumor board clinic at Indiana University. Aldy v3.3 was implemented in LifeOmic’s Precision Health Cloud™ to call PGx genotypes from somatic WES. Somatic Aldy calls were compared with previously validated Aldy germline calls for 8 genes: CYP2C9, CYP2C19, CYP2D6, CYP3A4, CYP3A5, CYP4F2, DPYD, and TPMT. Somatic read depth was &amp;gt;100x, except for the intronic CYP3A4*22 variant, which was &amp;gt;30x. Results Somatic and germline Aldy calls were compared for a total of 512 genotypes and 56 (11%) calls were discordant. Discordant calls were most common for CYP2B6 (23.4%), followed by CYP2D6 (14.1%), CYP2C19 (10.9%), CYP2C8 (6.3%), and DPYD (6.3%). In contrast, all Aldy calls were concordant for CYP3A5 and TPMT. 38 out of 64 subjects (59%) had discordant calls for at least one gene. The most common first cancer diagnoses in our cohort were colorectal (9.3%), breast (7.8%), and pancreatic (7.8%), and the rates of discordant Aldy calls did not differ by cancer type (p&amp;gt;0.05 for all cancer types). Based on our analyses of discordant calls, we anticipate that adjusting Aldy’s thresholds for variant calling may allow Aldy to determine genotypes from somatic WES data. Conclusion In most cases, genotype calls of drug metabolism genes from tumor DNA reflected the germline genotypes; however, additional work needs to be done to determine if the remaining discordant calls can be corrected by modifying the informatics tools or if they are due to somatic mutations. Citation Format: Wilberforce A. Osei, Tyler Shugg, Reynold C. Ly, Steven M. Bray, Benjamin A. Salisbury, Ryan R. Ratcliff, Victoria M. Pratt, Ibrahim Numanagić, Todd Skaar. Pharmacogenomics genotyping from clinical somatic whole exome sequencing: Aldy, a computational tool [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1151.

Abstract 1452: Analyses of whole exome sequencing (WES) data of hereditary lung cancer families identify germline copy number variations (CNVs) in multiple genes

Abstract Lung cancer (LC) is the most common cause of cancer mortality and the third most common cancer by incidence in the United States. While environmental factors play an important role in its development, LC risk also exhibits a high degree of heritability. Linkage analyses and genome-wide association studies have identified multiple loci associated with increased LC risk; however, much of the heritability has yet to be explained by these loci. Structural mutations, including copy number variations (CNVs), contribute to phenotypic diversity through dosage and/or cis-regulatory effects. Unbiased CNV mapping is only possible with the use of high-depth, short-read sequencing and remains much more complicated and prone to false positives than SNP detection. As the tools necessary for CNV detection have improved, both somatic and germline CNVs have been shown to play an important role in disease, especially cancer, and often they account for a significant proportion of pathogenic variants. Little has been done to understand the role of germline CNVs in the biological pathways of hereditary lung cancer (HLC). The goal of the current project is to utilize the whole exome sequencing (WES) data in identifying the CNVs in the HLC families (≥3 LC/family) recruited by the Genetic Epidemiology of Lung Cancer Consortium (GELCC). This work uses germline WES data from 203 individuals (60 with a LC diagnosis) from 25 HLC families (≥3 LC affected/family). We limited our investigation to CNVs called by two independent tools using read depth to infer copy number changes and genomic breakpoints: GATK 4 (https://gatk.broadinstitute.org) and XHMM (https://atgu.mgh.harvard.edu/xhmm/). We have identified CNVs (deletions) in the following protein coding genes: KIR2DL1 (19q13.42; OR=1.77), DMBT1 (10q26.13; OR=1.56), SIBPB1 (20p13; OR=1.53), LILRA6 (20p13; OR=1.53), and HLA-DRB5 (6p21.32; OR=1.64) in ≥3 families in at least two individuals/family. All of these genes with the exception of HLA-DRB5 were previously reported in LC studies; HLA-DRB5 was reported in other cancer studies. DMBT1 was reported to be a candidate tumor suppressor gene and frequent loss of heterozygosity (LOH) was observed in several human tumors. It is highly expressed in lung and loss of expression was reported in LC cell lines. All CNVs identified in our study are consistent with Mendelian expectations and appear to be uncommon in the general population. CNVs in these genes may contribute to the lung cancer risk in the HLC families. Further validation of the identified variants is ongoing. We will consider overall CNV burden and disease association with identified deletions and duplications. The enrichment of rare variants in oncogenically associated genes that co-segregate with LC provides specific mutations for future work and improves our understanding of the inheritance and pathogenesis of LC. Citation Format: John Waldron, Kirsten W. Termine, Anthony M. Musolf, Mariza de Andrade, Colette Gaba, Ramaswamy Govindan, Ping Yang, Ming You, Ellen Jaeger, Angelle F. Bencaz, Marshall W. Anderson, Ann G. Schwartz, Susan M. Pinney, Christopher I. Amos, Joan E. Bailey-Wilson, Diptasri M. Mandal. Analyses of whole exome sequencing (WES) data of hereditary lung cancer families identify germline copy number variations (CNVs) in multiple genes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1452.

Identifying germline genetic alterations or environmental factors associated with bilateral germ cell tumor (GCT).

5035 Background: Germline genomic alterations and/or environmental factors are proposed as critical to GCT development given the significant rates of bilateral and familial cases. A number of low-moderate risk loci for GCT have been identified (Litchfield, Eur Urol 2018 &amp; Pluta, Nat Comm 2021), predominantly by analysing unilateral GCT, with a polygenic heritability model proffered. We postulate bilateral GCT represents an extreme phenotype with higher frequency of loss of function germline genomic alterations and/or pre-disposing environmental exposures. Methods: Bilateral GCT pts who consented to a prospective clinically annotated GCT DNA registry were included for analysis. The registry integrates self-reported questionnaires on environmental exposures, relevant medical history and germline whole exome sequencing (WES). Pathogenicity of variants identified by WES were classified using the algorithm Pathogenicity of Mutation Analyzer (PathoMAN) [Ravichandran, Genet Med 2019]. Aggregated WES results were curated to identify disruptive or deleterious variants affecting the same genes as the most significant individual variants in the Litchfield series. A &lt; 1% minor allele frequency threshold was set for candidate variants, likely benign/benign variants were excluded . Results: Of 43 bilateral cases with germline WES results, median age at first diagnosis was 32.1 years (range 18-73), 9 tumors were synchronous and 34 metachronous with median interval between diagnosis of 76.4 months for metachronous cases. Tumor histology was seminoma in 52 and nonseminoma in 34. 39 of 43 (91%) pts completed questionnaires with 35 (90%) reporting White race, 2 Hispanic/Latino, 1 Asian, and 1 Peruvian. 13 (33%) reported prior smoking, 21 (54%) prior marijuana use, and 6 (15%) other illicit drug use. 6 (15%) pts reported undescended testis and 1 (3%) hypospadias. 24/43 (45%) patients harbored ≥1 variant within 15 Litchfield genes (60%). 43 distinct variants were identified: 33 (77%) nonsynonymous missense alterations, 7 (16%) intron variants, 1 inframe deletion in STH3TC1, and 1 initiator and 1 stop codon variant in DEFB132, which plays a role in binding spermatozoa. Multiple bilateral patients harbored variants in MPDZ (n = 7), EHBP1L1 (n = 6), SKIV2L (n = 5), FAM160A2 (n = 3), ADAMTS18 (n = 3), JMJD4 (n = 3), ABCC4 (n = 3), R3HCC1 (n = 2), MLXIP (n = 2) and VPS16 (n = 2). Conclusions: In this bilateral GCT cohort, we identified several alterations in candidate susceptibility genes from the Litchfield series, whereas no convincing causative recurrent environmental exposures were observed. Our results support a polygenic model of GCT pathogenesis and show that analyzing enriched cohorts such as bilateral GCT may aid understanding of GCT pathogenesis. Additional analysis of the specific variants is required to further assess pathogenicity, elucidate their role and association with bilateral GCT.

Case Review: Whole-Exome Sequencing Analyses Identify Carriers of a Known Likely Pathogenic Intronic BRCA1 Variant in Ovarian Cancer Cases Clinically Negative for Pathogenic BRCA1 and BRCA2 Variants.

Background: Detecting pathogenic intronic variants resulting in aberrant splicing remains a challenge in routine genetic testing. We describe germline whole-exome sequencing (WES) analyses and apply in silico predictive tools of familial ovarian cancer (OC) cases reported clinically negative for pathogenic BRCA1 and BRCA2 variants. Methods: WES data from 27 familial OC cases reported clinically negative for pathogenic BRCA1 and BRCA2 variants and 53 sporadic early-onset OC cases were analyzed for pathogenic variants in BRCA1 or BRCA2. WES data from carriers of pathogenic BRCA1 or BRCA2 variants were analyzed for pathogenic variants in 10 other OC predisposing genes. Loss of heterozygosity analysis was performed on tumor DNA from variant carriers. Results: BRCA1 c.5407-25T>A intronic variant, identified in two affected sisters and one sporadic OC case, is predicted to create a new splice effecting transcription of BRCA1. WES data from BRCA1 c.5407-25T>A carriers showed no evidence of pathogenic variants in other OC predisposing genes. Sequencing the tumor DNA from the variant carrier showed complete loss of the wild-type allele. Conclusions: The findings support BRCA1 c.5407-25T>A as a likely pathogenic variant and highlight the importance of investigating intronic sequences as causal variants in OC families where the involvement of BRCA1 is highly suggestive.

Solving the genetic aetiology of hereditary gastrointestinal tumour syndromes– a collaborative multicentre endeavour within the project Solve-RD

BackgroundPatients and families with suspected, but genetically unexplained (unsolved) genetic tumour risk syndromes lack appropriate treatment and prevention, leading to preventable morbidity and mortality. To tackle this problem, patients from the European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS) are analysed in the European Commission's research project “Solving the unsolved rare diseases” (Solve-RD). The aim is to uncover known and novel cancer predisposing genes by reanalysing available whole-exome sequencing (WES) data of large cohorts in a combined manner, and applying a multidimensional omics approach. ApproachAround 500 genetically unsolved cases with suspected hereditary gastrointestinal tumour syndromes (polyposis, early-onset/familial colorectal cancer and gastric cancer) from multiple European centres are aimed to be included. Currently, clinical and germline WES data from 294 cases have been analysed. In addition, an extensive molecular profiling of gastrointestinal tumours from these patients is planned and deep learning techniques will be applied. The ambitious, multidisciplinary project is accompanied by a number of methodical, technical, and logistic challenges, which require the development and implementation of new analysis tools, the standardisation of bioinformatics pipelines, and strategies to exchange data and knowledge. Resultsand Outlook. The first re-analysis of 229 known and proposed cancer predisposition genes allowed solving 2–3% of previously unsolved GENTURIS cases. The integration of expert knowledge and new technologies will help to identify the genetic basis of additional unsolved cases within the ongoing project. The ERN GENTURIS approach might serve as a model for other genomic initiatives.

Prevalence of (Epi)genetic Predisposing Factors in a 5-Year Unselected National Wilms Tumor Cohort: A Comprehensive Clinical and Genomic Characterization.

PURPOSEWilms tumor (WT) is associated with (epi)genetic predisposing factors affecting a growing number of WT predisposing genes and loci, including those causing Beckwith-Wiedemann spectrum (BWSp) or WT1-related syndromes. To guide genetic counseling and testing, we need insight into the prevalence of WT predisposing (epi)genetic factors.PATIENTS AND METHODSAll children diagnosed with WT in the Netherlands between 2015 and 2020 were referred to a clinical geneticist. Phenotypic data, disease characteristics, and diagnostic test results were collected. If no genetic predisposition was identified by targeted diagnostic testing, germline (trio-)whole-exome sequencing and BWSp testing on normal kidney-derived DNA were offered.RESULTSA total of 126 cases were analyzed of 128 identified patients. (Epi)genetic predisposing factors were present in 42 of 126 patients (33.3%) on the basis of a molecular diagnosis in blood-derived DNA (n = 26), normal kidney-derived DNA (n = 12), or solely a clinical diagnosis of BWSp (n = 4). Constitutional, heterozygous DIS3L2 variants were identified as a recurrent predisposing factor in five patients (4%), with a second somatic hit in 4 of 5 tumors. Twenty patients (16%) were diagnosed with BWSp while four additional patients without BWSp features harbored chromosome 11p15 methylation defects in normal kidney tissue. Remaining findings included WT1-related syndromes (n = 10), Fanconi anemia (n = 1), neurofibromatosis type 1 (n = 1), and a pathogenic REST variant (n = 1). In addition, (likely) pathogenic variants in adult-onset cancer predisposition genes (BRCA2, PMS2, CHEK2, and MUTYH) were identified in 5 of 56 (8.9%) patients with available whole-exome sequencing data. Several candidate WT predisposition genes were identified, which require further validation.CONCLUSION(Epi)genetic WT predisposing factors, including mosaic aberrations and recurrent heterozygous DIS3L2 variants, were present in at least 33.3% of patients with WT. On the basis of these results, we encourage standard genetic testing after counseling by a clinical geneticist.

Abstract P1-08-02: Cytochrome P450 reductase gene, POR, associated with paclitaxel induced peripheral neuropathy in patients of European ancestry from the adjuvant breast cancer trial, ECOG-ACRIN E5103

Abstract Introduction: Paclitaxel induced peripheral neuropathy (TIPN) is one of the most important survivorship issues of cancer patients with the potential to substantially impact quality of life. TIPN can lead to dose reductions, early cessation, and has the potential to compromise treatment efficacy. We previously reported both rare (SBF2) and common germline (FCAMR) predictors for TIPN in patients of African descent through whole-exome sequencing (WES) and a genome-wide association study (GWAS), respectively, in the adjuvant, randomized phase III breast cancer trial, E5103. These predictors are now being evaluated in the prospective ECOG-ACRIN trial EAZ171 (NCT04001829). We have also previously reported our evaluation of common germline variants for patients of European descent through GWAS in E5103 with validation in another adjuvant breast cancer trial, E1199. Herein, we evaluated for rare variants that were associated with risk of TIPN in patients of European ancestry from WES in E5103. Methods: Gene-based rare variant analyses using SKAT were performed to compare select cases of severe TIPN (n=172) and controls without any evidence of TIPN (n=170) derived from E5103. Cases were defined as those with at least grade 3 TIPN and controls were optimally. matched by demographic and risk factors and had no reported evidence for TIPN of any grade. Germline WES was conducted using Ion Proton™ Sequencers from Life Technologies with an average &amp;gt;100X coverage of the exome. Rare variants with a minor allele frequency &amp;lt;3% predicted to be deleterious by protein prediction programs were retained for the analysis. 7,278 genes passed quality control and were included in the analysis, setting the threshold for significance at a p-value &amp;lt; 6.87 ×10-6 after Bonferroni correction. Results: Cytochrome P450 oxidoreductase (POR) was significantly associated with an increased risk of grade 3+ TIPN (p =1.82 ×10-6). Six variants predicted to be deleterious in POR were identified in the study population. Paclitaxel is predominately metabolized by cytochrome P450 (CYP) 2C8 and 3A4. A functional cytochrome P450 oxidoreductase is required for the catalytic activities of all 57 CYP family members to metabolize drugs, xenobiotics, and steroid hormones. Conclusion: Rare variants in cytochrome P450 oxidoreductase predicted an increased risk of severe TIPN in patients receiving paclitaxel. These rare variants in POR may modulate the catalytic activities of P450 enzymes that are responsible for paclitaxel metabolism and have a striking biological rationale as contributors to TIPN. Work is ongoing to validate these findings mechanistically and to identify strategies to nullify the impact of these deleterious variants. Citation Format: Fei Shen, Guanglong Jiang, Laura Gardner, Gloria Xue, Santosh Philips, Reynold Ly, Osei Wilberforce, Xi Wu, Erica Cantor, Chau Dang, Donald Northfelt, Todd Skaar, Kathy D. Miller, George Sledge, Bryan P Schneider. Cytochrome P450 reductase gene, POR, associated with paclitaxel induced peripheral neuropathy in patients of European ancestry from the adjuvant breast cancer trial, ECOG-ACRIN E5103 [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P1-08-02.

Whole-Exome Sequencing in Multiplex Families to Identify Novel AYA Classical Hodgkin Lymphoma Predisposition Genes

Background:Hodgkin Lymphoma (HL) is a B-cell malignancy that mainly affects young adults in economically developed countries. Classical HL (cHL) is the most common type, comprising >95% of cases. We demonstrated strong heritability of cHL in adolescents and young adults (AYA) with a high risk to the unaffected co-twins of affected monozygotic (MZ) twins. We and others identified common risk variants by GWAS, and sequencing of familial and sporadic HL patients previously identified rare pathogenic germline variants in genes with varying functions. Few have replicated in other families. A greater understanding of the genes involved in cHL predisposition is needed. We performed germline whole-exome sequencing (WES) for 48 individuals in 14 multiplex families with AYA cHL patients to identify novel cHL predisposition genes.Methods:Index cases from multiplex families were ascertained from the USC twin registries (International Twin Registry or California Twin Program, 7 index cases, 2 additional cases, and 7 unaffected relatives) or from the USC Cancer Surveillance Program (7 index cases, 4 additional cases, and 21 unaffected relatives). Among the twin pairs, 5 were concordant MZ pairs, one was a concordant dizygotic pair and one was an MZ discordant pair with a second case occurring in the daughter of the unaffected MZ co-twin. The other 7 families included 4 with two affected siblings, one with a child/father pair, and two with child/uncle pairs; the latter 3 families had specimens available for the index child case only. All index cases were diagnosed under 50 years old, with the median age 27.DNA samples were extracted from blood or saliva of 48 individuals in 14 multiplex families, with specimens from 20 of 28 reported cases. Germline WES was performed using the Nextera® Rapid Capture Exome kit, with data pre-processing performed based on Genome Analysis Toolkit best practices guidelines, and additional filtering applied using BCFtools. Variants were annotated using ANNOVAR. We filtered out variants with an allele frequency >0.001 in population databases (gnomAD or TOPMed), and variants documented as benign/likely benign in ClinVar. We retained splicing/ncRNA variants and exonic variants with loss-of-function/missense/unknown functional consequences, and with a CADD score >10. We further limited variants to those in 1,073 candidate predisposition genes, including cancer/immunodeficiency/hematological-related genes in the Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE) and genes previously identified in sequencing studies or GWAS for cHL. Variants in candidate genes were visually inspected in the Integrative Genomics Viewer and were analyzed for their potential pathogenicity through the PeCanPIE MedalCeremony pipeline. Variants predicted to be tolerated by PeCanPIE were removed. Variants found only in HL patients and not in their sibling controls were considered to be potentially causal.Results:In 45 subjects that passed sequencing QC (3 controls were removed due to low mean coverage) and following variant filtering, there were 33 variants in 33 genes found only in cHL patients but not in their sibling controls, among 9 of 14 families. None of the variants appeared in more than one family.One variant in PGK1 was previously reported as pathogenic/likely pathogenic in ClinVar in patients with phosphoglycerate kinase 1 deficiency associated with hemolytic anemia. Nine variants were reported in ClinVar as variants of uncertain significance, of which 3 were previously reported in patients with immunodeficiency disorders (in genes IL2RA, MALT1, and PRKDC) and 2 were reported in patients with dyskeratosis congenita (TERT) and other anemia-associated disorders (EPB42). Of 22 variants not reported in ClinVar, one was a missense variant in NPAT, a gene previously associated with familial lymphoma; 4 were in genes associated with immune disorders (PLCG2, LIG1, C1QB, and NOD2) and 3 were in genes associated with anemia (SPTB, ALDOA, and GATA1). To our knowledge, none of these genes other than NPAT have previously been implicated in predisposition to HL.Conclusions:WES in 20 AYA cHL patients among multiplex families identified putative novel predisposition genes for HL, including genes implicated in anemia and immune function. Assessment of these genes in sequencing studies of independent HL families is required to understand their role in HL predisposition. DisclosuresWadé: Flatiron Health: Current Employment; Roche: Current equity holder in publicly-traded company.

Real-World Evaluation of Universal Germline Screening for Cancer Treatment-Relevant Pharmacogenes.

Simple SummaryGermline pharmacogenomic variants impact the toxicity of many cancer treatment drugs. Though testing for pharmacogenomic variants prior to initiating systemic cancer treatment is not routine, the Clinical Pharmacogenetics Implementation Consortium recommends dosing modifications for six cancer treatment drugs based on variant genotypes: irinotecan and UGT1A1; 5-fluorouracil and capecitabine and DPYD; 6-mercaptopurine and thioguanine and TPMT; and tamoxifen and CYP2D6. The purpose of this study was to assess the frequency of cancer treatment-relevant germline pharmacogenomic variants in patients with cancer using residual germline whole-exome sequencing. We also evaluated the association of disease-relevant pharmacogenomic variants with treatment-associated toxicities. Approximately one-quarter of cancer patients carried a disease-relevant pharmacogenomic variant. Patients with toxicity-associated pharmacogenomic variant genotypes were more likely to experience drug-related toxicity than their wild-type counterparts. Universal pharmacogenomic screening is feasible using whole-exome sequencing originally obtained for quality control purposes and may be an effective germline pharmacogenomic screening strategy for patients who are candidates for irinotecan, 5-fluorouracil, capecitabine, or 6-mercaptopurine. The purpose of this study was to determine the frequency of clinically actionable treatment-relevant germline pharmacogenomic variants in patients with cancer and assess the real-world clinical utility of universal screening using whole-exome sequencing in this population. Cancer patients underwent research-grade germline whole-exome sequencing as a component of sequencing for somatic variants. Analysis in a clinical bioinformatics pipeline identified clinically actionable pharmacogenomic variants. Clinical Pharmacogenetics Implementation Consortium guidelines defined clinical actionability. We assessed clinical utility by reviewing electronic health records to determine the frequency of patients receiving pharmacogenomically actionable anti-cancer agents and associated outcomes. This observational study evaluated 291 patients with cancer. More than 90% carried any clinically relevant pharmacogenetic variant. At least one disease-relevant variant impacting anti-cancer agents was identified in 26.5% (77/291). Nine patients with toxicity-associated pharmacogenomic variants were treated with a relevant medication: seven UGT1A1 intermediate metabolizers were treated with irinotecan, one intermediate DPYD metabolizer was treated with 5-fluorouracil, and one TPMT poor metabolizer was treated with mercaptopurine. These individuals were more likely to experience treatment-associated toxicities than their wild-type counterparts (p = 0.0567). One UGT1A1 heterozygote died after a single dose of irinotecan due to irinotecan-related adverse effects. Identifying germline pharmacogenomic variants was feasible using whole-exome sequencing. Actionable pharmacogenetic variants are common and relevant to patients undergoing cancer treatment. Universal pharmacogenomic screening can be performed using whole-exome sequencing data originally obtained for quality control purposes and could be considered for patients who are candidates for irinotecan, 5-fluorouracil, capecitabine, and mercaptopurine.

Potential Role for the RASD1 Glucocorticoid-Responsive Gene in Corticotroph Tumorigenesis

Introduction: Originally identified due to its dexamethasone inducibility in mouse corticotropinoma AtT20 cells, RASD1 is a receptor-independent activator of G-proteins, via guanine nucleotide exchange factor (GEF) activity. It remains unclear, however, whether, and if so, how RASD1 mediates the effects of glucocorticoids on corticotroph cells. We identified a rare germline RASD1 variant and investigated its functional effects in vitro. Methods: We screened 209 CD patients (94.3% pediatric) studied at the at the National Institutes of Health Clinical Research Center between 1997 and 2018 by germline whole-exome sequencing (WES) only (n=157), germline and tumor WES (n=27), and/or RASD1 droplet digital PCR germline copy number variant (CNV) analysis (n=201). Corticotropinoma DNA was available in 72 patients to screen for USP8 hotspot variants by Sanger sequencing. A RASD1 variant was identified and functionally characterized. Results: We studied 119 female (56.9%) and 90 (43.1%) male CD cases, including 197 pediatric (≤18 years at disease onset) and 12 adult patients. USP8 defects were present in 19.4% (14/72) of cases. No RASD1 CNVs were found. A rare (with a minor allele frequency of 0.0022% in gnomAD v3) heterozygous germline missense RASD1 variant, c.580A>C, p.M194L was detected in one male sporadic case. Neither USP8 variants nor loss of heterozygosity at the RASD1 variant position were observed in the patient’s microadenoma. The wild type and p.M194L RASD1 transiently overexpressed proteins displayed similar short half-lives (<1 h) by cycloheximide chase in HEK293 cells, as well as cytoplasmic localization by immunocytofluorescence in AtT20 cells. A CRISPR/Cas9 Rasd1 knockout AtT20 cell line displayed reduced Pomc expression compared with the parental cell line at the mRNA level (Actb-normalized absolute quantification 5.80±0.92 vs 9.62±0.7, P=0.005). Viability of the cell lines did not differ significantly by MTT assay. Overexpression of p.M194L resulted in increased accumulation of phospho-CREB S133 (1.83±0.8 vs 1±0.2 in empty vector control, P=0.0390) as well as a non-significant increase in Pomc expression in wild type, but not in Rasd1 knockout AtT20 cells by immunoblot band densitometry. Conclusions: We found an infrequent RASD1 variant in one CD patient. Rasd1 seems to have a role within the intracellular signaling pathways controlling Pomc expression. Overexpression of the p.M194L variant caused phospho-CREB S133 activation, suggesting increased GEF activity for this variant. Interestingly, another variant at the same position, p.M194I, was found in the COSMIC database (COSS2121715) as a somatic change in cutaneous malignant melanoma. Further studies are required to better define the role of RASD1 in corticotroph physiology and its possible involvement in tumorigenesis.