Germline Mutation Rate Research Articles

Effective Population Size Predicts Local Rates but Not Local Mitigation of Read-through Errors.

In correctly predicting that selection efficiency is positively correlated with the effective population size (Ne), the nearly neutral theory provides a coherent understanding of between-species variation in numerous genomic parameters, including heritable error (germline mutation) rates. Does the same theory also explain variation in phenotypic error rates and in abundance of error mitigation mechanisms? Translational read-through provides a model to investigate both issues as it is common, mostly nonadaptive, and has good proxy for rate (TAA being the least leaky stop codon) and potential error mitigation via “fail-safe” 3′ additional stop codons (ASCs). Prior theory of translational read-through has suggested that when population sizes are high, weak selection for local mitigation can be effective thus predicting a positive correlation between ASC enrichment and Ne. Contra to prediction, we find that ASC enrichment is not correlated with Ne. ASC enrichment, although highly phylogenetically patchy, is, however, more common both in unicellular species and in genes expressed in unicellular modes in multicellular species. By contrast, Ne does positively correlate with TAA enrichment. These results imply that local phenotypic error rates, not local mitigation rates, are consistent with a drift barrier/nearly neutral model.

Clinical Characteristics and Mutation Analyses of Ovarian Sertoli-Leydig Cell Tumors.

There are limited studies on Sertoli-Leydig cell tumors (SLCTs) and no data in the population of Chinese patients with SLCTs from the genetic level. In addition, previous studies on SLCTs have focused exclusively on mutations in the DICER1 gene and no data exists on the genetic landscape of SLCTs. Patients with moderately or poorly differentiated SLCTs who underwent surgical resection between January 2012 and October 2018 in our institution were recruited. Whole exome sequencing was performed on formalin-fixed, paraffin-embedded tumor tissue and peripheral blood or normal tissue samples. Seventeen patients were recruited with 19 tumor samples. The rate of tumor-associated germline mutations was 6 of 17 (35.3%), and that of DICER1 germline mutations was 4 of 17 (23.5%). Regarding clinical relapse, patients with germline tumor-associated mutations had significantly poorer prognosis than those without (p = .007), and those with germline DICER1 mutations were relatively more likely to exhibit clinical relapse, although not to a significant degree (p = .069). Regarding somatic mutations, firstly, the subclone evolution analysis demonstrated that the two tumors on the contralateral ovary were primary tumors, respectively. Secondly, somatic mutations were most commonly found in CDC27 (10/19, 52.6%), DICER1 (4/19, 21.1%), and MUC22 (4/19, 21.1%). And the analysis of cancer cell fractions showed that DICER1 mutations were correlated with tumorigenesis of SLCTs. The rates of germline and somatic DICER1 mutations were higher in patients who were younger than 18 years than those in older patients (p = .022 and p = .001, respectively). Our study indicates that genetic testing may have important clinical significance for patients with SLCTs, particularly for younger patients. Bilateral ovarian Sertoli-Leydig cell tumors were verified to be primary tumors from the genetic perspective. The rates of germline and somatic DICER1 mutations were 4 of 17 (23.5%) and 4 of 19 (21.1%), respectively. The rates of germline and somatic DICER1 mutations were higher in patients who were younger than 18 years than those in older patients (p = .022 and p = .001, respectively).

High-Efficiency CRISPR/Cas9 Mutagenesis of the white Gene in the Milkweed Bug Oncopeltus fasciatus.

In this manuscript, we report that clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 is highly efficient in the hemipteran Oncopeltus fasciatus. The white gene is well characterized in Drosophila where mutation causes loss of eye pigmentation; white is a reliable marker for transgenesis and other genetic manipulations. Accordingly, white has been targeted in a number of nonmodel insects to establish tools for genetic studies. Here, we generated mutations in the Of-white (Of-w) locus using CRISPR/Cas9. We found that Of-w is required for pigmentation throughout the body of Oncopeltus, not just the ommatidia. High rates of somatic mosaicism were observed in the injected generation, reflecting biallelic mutations, and a high rate of germline mutation was evidenced by the large proportion of heterozygous G1s. However, Of-w mutations are homozygous lethal; G2 homozygotes lacked pigment dispersion throughout the body and did not hatch, precluding the establishment of a stable mutant line. Embryonic and parental RNA interference (RNAi) were subsequently performed to rule out off-target mutations producing the observed phenotype and to evaluate the efficacy of RNAi in ablating gene function compared to a loss-of-function mutation. RNAi knockdowns phenocopied Of-w homozygotes, with an unusual accumulation of orange granules observed in unhatched embryos. This is, to our knowledge, the first CRISPR/Cas9-targeted mutation generated in Oncopeltus. While we were unable to establish white as a useful visible marker for Oncopeltus, these findings are instructive for the selection of visible markers in nonmodel species and reveal an unusual role for an ortholog of a classic Drosophila gene.

Inherited mutations in fallopian tube, ovarian and primary peritoneal carcinoma: Changes in diagnoses and mutational frequency over 20 years

ObjectivesWomen with fallopian tube carcinoma (FTC) are reported to have a higher frequency of inherited BRCA mutations than those with ovarian carcinoma (OC) or primary peritoneal carcinoma (PPC). We hypothesized that routine serial sectioning of fallopian tubes would increase the proportion of cases designated as FTC and change the frequency of inherited mutations between carcinoma types. MethodsEight hundred and sixty-seven women diagnosed from 1998 to 2018 were enrolled at diagnosis into an institutional tissue bank. Germline DNA, available from 700 women with FTC (N = 124), OC (N = 511) and PPC (N = 65), was assessed using targeted capture and massively parallel sequencing for mutations in ovarian carcinoma susceptibility genes. Cases were divided between those prior to routine serial sectioning (1998–2008) and after (2009–2019), and the frequency of FTC and inherited mutations was assessed. ResultsThe proportion of carcinomas attributed as FTC after 2009 was 28% (128/465), significantly higher than before 2009 [5% (21/402), p < .0001, OR 6.9, 95% CI 4.3–11.2], with subsequent decreases in OC and PPC. In the sequenced group, overall inherited mutation frequency in FTC (24/124, 19%), OC (106/511, 21%, p = .42), and PPC (16/65, 25%, p = .25) were similar. Germline mutation rates in FTC were lower after 2009,16/107 cases (15%), compared to 8/17 cases (47.1%) before 2009 (p = .005, OR 0.20, 95% CI 0.06–0.64). ConclusionsThe prevalence of inherited mutations is similar in FTC compared to OC or PPC when using modern pathological assignment. Complete serial sectioning of fallopian tubes has significantly increased the diagnosis of FTC, and subsequently decreased the frequency of inherited mutations within this group.

Higher Germline Mutagenesis of Genes with Stronger Testis Expressions Refutes the Transcriptional Scanning Hypothesis.

Why are more genes expressed in the testis than in any other organ in mammals? The recently proposed transcriptional scanning hypothesis posits that transcription alleviates mutagenesis through transcription-coupled repair so has been selected in the testis to modulate the germline mutation rate in a gene-specific manner. Here, we show that this hypothesis is theoretically untenable because the selection would be too weak to have an effect in mammals. Furthermore, the analysis purported to support the hypothesis did not control known confounding factors and inappropriately excluded genes with no observed de novo mutations. After remedying these problems, we find the human germline mutation rate of a gene to rise with its testis expression level. This trend also exists for inferred coding strand-originated mutations, suggesting that it arises from transcription-associated mutagenesis. Furthermore, the testis expression level of a gene robustly correlates with its overall expression in other organs, nullifying the need to explain the testis silencing of a minority of genes by adaptive germline mutagenesis. Taken together, our results demonstrate that human testis transcription increases the germline mutation rate, rejecting the transcriptional scanning hypothesis of extensive gene expressions in the mammalian testis.

Germline mutation rates in young adults\xa0predict longevity and reproductive lifespan

Ageing may be due to mutation accumulation across the lifespan, leading to tissue dysfunction, disease, and death. We tested whether germline autosomal mutation rates in young adults predict their remaining survival, and, for women, their reproductive lifespans. Age-adjusted mutation rates (AAMRs) in 61 women and 61 men from the Utah CEPH (Centre d’Etude du Polymorphisme Humain) families were determined. Age at death, cause of death, all-site cancer incidence, and reproductive histories were provided by the Utah Population Database, Utah Cancer Registry, and Utah Genetic Reference Project. Higher AAMRs were significantly associated with higher all-cause mortality in both sexes combined. Subjects in the top quartile of AAMRs experienced more than twice the mortality of bottom quartile subjects (hazard ratio [HR], 2.07; 95% confidence interval [CI], 1.21–3.56; p = 0.008; median survival difference = 4.7 years). Fertility analyses were restricted to women whose age at last birth (ALB) was ≥ 30 years, the age when fertility begins to decline. Women with higher AAMRs had significantly fewer live births and a younger ALB. Adult germline mutation accumulation rates are established in adolescence, and later menarche in women is associated with delayed mutation accumulation. We conclude that germline mutation rates in healthy young adults may provide a measure of both reproductive and systemic ageing. Puberty may induce the establishment of adult mutation accumulation rates, just when DNA repair systems begin their lifelong decline.

Genetic analysis of tri-allelic patterns at the CODIS STR loci.

In the routine of autosomal STR genotyping for forensic aims, tri-allelic patterns could be occasionally observed at a single locus in phenotypically normal individuals. Two predominant types of tri-allelic variants have been nominated. Uneven intensities of three alleles are normally considered as the Type 1 pattern, and balanced height of three alleles are considered as the Type 2 pattern. In this study, the prevalence of tri-allelic patterns at the CODIS STR loci was investigated in global populations based on previous reports. The frequencies of the Type 1 and Type 2 pattern manifest a correlation with the germline mutation rates at the CODIS STR loci. The irregular high frequencies of the Type 2 pattern at TPOX with low germline mutation rates could attribute to the stable inheritance of genomic rearrangement from ancestral origin. Furthermore, results from genetic pattern analysis show that only a single allele from STRs with the Type 1 pattern could be transmitted from parents to offsprings, while a single allele and a combination of two alleles from STRs with the Type 2 pattern present an equal opportunity of transmission from parents to offsprings. Altogether, these results provide a genetic portrait of STRs with tri-allelic patterns, which will help the genetic interpretation of tri-allelic patterns in forensic practice.

Streamlining the genetics pipeline to increase testing for patients at risk for hereditary prostate cancer.

1590 Background: Metastatic prostate Cancer (mPCa) is increasingly recognized as a heritable disease and germline genetic testing has increasingly become a part of standard of care. At the University of California at San Francisco (UCSF) Genitourinary (GU) Medical Oncology clinic, approximately 850 new patients with mPCa are seen annually. A feasibility pilot Genetic Testing Station (GTS) was developed to expand access to genetic testing among this high-risk population. GTS is facilitated by Genetic Counselor Assistants (GCA) under the supervision of genetic counselors. Methods: This is a feasibility pilot of a GTS model among patients with mPCa. In this model, all patients with mPCa are offered a same day GTS visit with a GCA. At the GTS, the patient receives pre-test education via videos developed by genetic counselors. The patient provides informed consent, a family history, and a saliva sample for Invitae’s 87-gene panel. All positive results trigger a genetic counselor visit while non-positive results either receive a letter or a genetic counselor visit (in person or via telehealth). To evaluate the model, testing frequency and laboratory turnaround time (TAT) was assessed before and after the pilot. Results: In the first four months of the GTS pilot (10/14/2019 – 02/10/2020), 94 patients were referred and received genetic testing. Eight germline positives were identified (BRCA2, CHEK2, HOXB13 MSH6, RECQL4). The average TAT was 8 days. 9.3% of patients were found to have pathogenic mutations through the prostate GTS which is comparable to previously published rates of germline mutations in metastatic prostate cancer patients. In a 4-month time frame the prior to the intervention (10/01/2018-1/31/2019), 26 genetic testing orders were placed. The average laboratory TAT in this prior process was 17 days. Rates of positive germline mutations in the prior model was 8.6%. Conclusions: The GTS is a feasible method to increase access to germline genetic testing among a high-risk population. It may reduce barriers to testing and facilitate real-time discussion of treatment and prevention strategies with patients and family members. As a result, we will continue to operate the GTS. This model provides a framework for scaling access for and cascade testing in other high-risk patient groups.

Germline mutations in DNA repair genes in a large series of unselected Chinese prostate cancer patients.

e17523 Background: Germline DNA repair gene (DRG) mutations has emerged as a potential determinant of cancer risk and therapeutic response in PCa. Despite substantial advances in delineating the germline mutation in DRGs among Caucasian population, the prevalence of mutations in DRGs are largely unknown among a large series of unselected prostate cancer patients in Chinese population. Methods: We enrolled 1003 prostate cancer patients from three different hospitals in China, unselected for family history of cancer or age at diagnosis. All patients received germline genetic testing using a clinician-selected multi-gene panel. The 18 DNA repair genes and HOXB13, which has established or emerging potential clinical actionability in PCa, were analyzed in our study. Results: A total of 94 (9.7%) deleterious germline mutations were identified among the 1003 unselected prostate cancer patients. Of these, 5.6% patients carried a BRCA1 or BRCA2 mutations (5.2% in BRCA2 and 0.4% in BRCA1), 3.6% patients carried other DRG mutations (including 10 genes) and 0.5% patients carried HOXB13 mutations. Besides, variants with uncertain significance (VUS) were found in approximately 45% patients. We also divided 633 metastatic PCa patients into 542 de novo metastastic PCa and 91 recurrent metastastic PCa and found mutation frequencies did not differ between these two groups (9.0% vs 11.6%, p = 0.6). Patients with younger age of onset or family history of cancers were more likely to harbour germline mutations in DRGs. However, the rate of germline mutations were still at a high level for patients more than 70 years old (6.7%) and patients without family history of cancers (7.5%). There is no statistically significant difference in the mutation frequencies between patients with metastasis and without metastasis (7.5% vs 9.2%, p = 0.4), which may be because 85% patients without metastasis in our cohort were in high to very high risk group or have lymph node metastasis. Conclusions: To our knowledge, our study reported the largested series of Chinese PCa patients who received germline genetic testing. Our study provided a rationality for germline genetic testing criteria from high risk to metastastic PCa regardless of family history considering the high proportion. In addition, we recommended a multigene panel covering 13 genes ( ATM, BRCA1, BRCA2, CHEK2, FANCA, HOXB13, MSH2, MSH6, NBN, PALB2, RAD51C, RAD51D, TP53) in China. Nevertheless, the high prevalence of VUS (45%) in Chinese PCa patients warrant further efforts.

Characterization of mutations in HRR genes, TMB, and PD-L1 expression in Chinese patients with ovarian cancer.

e18048 Background: A great number of clinical studies have confirmed the promising efficacy of ICIs and PARPi in multiple solid tumors. Here we aim to investigate the biomarkers related to these emerging therapies, including mutations in DNA homologous recombination repair (HRR) genes, tumor mutation burden (TMB) and PD-L1 expression in Chinese patients (pts) with ovarian cancer. Methods: A total of 209 pts with ovarian cancer were enrolled. Matched tumor-normal NGS of 1021 cancer-related genes was performed in 98 pts (T: 71 pts, T+B: 25 pts, B: 2 pts). Germline variants in ovarian cancer susceptibility genes were analyzed in 209 pts. PD-L1 expression was assessed by immunohistochemistry (Dako 22C3). Pts with TPS≥50 were considered as high expression and pts with 1≤TPS&lt;50 was considered as expression. Tissue TMB was calculated as the number of somatic non-synonymous SNVs and Indels per Mb in the coding region (with VAF ≥0.03). The threshold of TMB-high was 5.76 muts/MB. Results: Germline pathogenetic or likely pathogenetic variants were identified in 28.7% of pts ( BRCA1 15.3%, BRCA2 7.7%, RAD51D 2.0%, PALB2 1.0%, and 0.7% for CHEK2, MSH2, RAD51C and MSH6). Germline variants in HRR genes was identified in 27.3% of pts. The mutation detection rates in 96 tissue samples from surgery or biopsy and 25 ctDNA samples collected at disease recurrence were 100% and 96%, respectively. An average of 34.6% of tissue-derived mutations can be identified in ctDNA, and 55.2% of tissue-derived actionable mutations were observed in ctDNA. Besides, there were 83 private mutations, including PPMID (5), ARID2 (3), CHEK2 (3), PIK3CA (3) and ARID1B (2). Mutations in HRR genes were found in 36.5% (35/96) of tissue samples, and 12 pts harbored more than one HRR mutations. The detection rate of HRR mutations in ctDNA was 40% (10/25), and cases harbored more than one HRR mutations. The status of TMB and PD-L1 was analyzed in 30 pts. Two pts were evaluated as PD-L1 highly expressed and 9 pts were considered as expressed. Eight pts were assessed as TMB-high. Five pts with PD-L1 negative expression were TMB-high, and 8 pts with TMB-low were PD-L1 positive expression. TMB and PD-L1 expression are independent indicators with the spearman r of 0.01 (p = 0.96). Conclusions: The detection rate of germline and somatic mutations in HRR genes were 27.3% and 36.5-40%, respectively, which defined a large number of ovarian cancer pts who can benefit from PARPi. PD-L1 expression and TMB are independent biomarkers, which may be combined to predict the efficacy of immunotherapy in future exploratory trials.

Population genetic screening for hereditary breast and ovarian cancer in at-risk patients: A novel testing and prevention model for community hospitals reveals high mutation rates rurally.

1575 Background: Genetic testing for at risk non-cancer patients continues to increase (Guo F, et al Cancer 2020). We identified a high risk of familial breast and ovarian cancer in rural eastern North Carolina, and created a systematic approach for genetic screening, counseling and testing. Methods: A family history questionnaire was designed to assess for the risk for hereditary breast and ovarian cancer (HBOC) using NCCN guidelines, and used at key intake points within the unaffected population to determine eligibility for genetic testing. First it was offered at the time of all mammograms. Second, we offered it in the primary gynecology care setting to capture younger patients not participating in screening mammography. Patients meeting HBOC criteria were sent a letter and two phone calls to schedule genetic counseling. Analysis via descriptive statistics. Results: 3000 rural women screened using our systematic approach to genetic risk assessment. 22.4% (673/3000) of female patients met NCCN criteria for HBOC panel testing. All offered consultation and counseling. With a backlog to see patients due to higher than expected accrual, 217 patients have completed pre-test genetic counseling, 201 completed local 19-gene panel test, and 201 had post-test counseling. Germline mutations (=&gt;1) that predict for genetic susceptibility to cancer(s) occur in 7.8% of our screened and tested population. Currently 1 in 400 patients screened in our unaffected population carry a BRCA mutation, and 1 in 200 carry some pathogenic mutation that increases risk for HBOC. Conclusions: This rural model of screening and prevention of at risk patients for HBOC is successful at detecting pathogenic mutations in unaffected patients before they are diagnosed with cancer. Interestingly, the rate of positivity in the unaffected population (meeting criteria) is as high as the known breast cancer population rate of germline mutations (5-10%), validating the use of testing guidelines with our model. Discovering this susceptibility before a cancer diagnosis resulted in appropriate high risk management with prevention and risk reduction strategies. We plan to expand this model to the male screening population in 2021, and streamline genetic assessment and testing for the larger population at risk by engaging more rural primary care clinics over time to increase testing compliance. We also plan to consider broader gene panels as newer mutations become linked to HBOC. Clinical trial information: UMCIRB 19-001052.

Evaluating the clinical, environmental, genetic, and genomic profile of men with early-onset aggressive prostate cancer (PCa).

e17517 Background: Although PCa incidence has stabilized/decreased in most age groups, the incidence of metastatic disease has increased among men 50-69 years-old. The incidence of fatal PCa has decreased for most age groups, it has remained unchanged in men under 55 years-old. Studies have described genetic abnormalities in aggressive localized or end-stage PCa, but early-onset cases are not included or are under-represented. The primary objective of this study is to characterize the clinical, environmental, genetic and genomic features of high-risk advanced PCa. Methods: Study cohort includes men with PCa ≤ 60 years old with N1 or M1 stage at diagnosis or who develop metastases in 5-years after local therapy. Clinical (race, family history (Hx), environmental exposure), laboratory,/pathology, cell-free DNA germline analysis were collected. Primary/metastatic tumor tissue tested via the Tempus-Xe platform (DNA sequencing, whole transcriptome expression profiling, copy number analysis, comprehensive fusion gene analysis and calculation of tumor mutational burden). We report interim analysis. Results: Study completed accrual with 30 pts. Median age 55 years (41-60), 87% are white, 13% are black, 77% had a family Hx of malignancy in 1-6 family members, including 40% with family hx of PCa. Only 33% had Hx of smoking. Median Gleason score 9. Only 27% had nodal disease, and 73% had metastatic disease at diagnosis. Molecular data are available in 25 pts. Most common germline mutations: BRCA2 (12%), ATM (12%), RB1 (8%), MSH3 (8%) and MYBPC3 (8%). Most common somatic mutations:TP53 (40%), TMPRSS2-ERG fusion (32%), MUC4 (16%), PTEN (12%), C2CD4D (12%), SPOP (12%), OBSCN (12%), MXRA5 (12%), and MYO15A (12%). Microsatellite stability status was available in 15 pts and all were stable. Tumor mutational burden was low in all pts, ranging between 0.7 to 2.7 mutations/megabase. Conclusions: Our preliminary data suggest high rates of germline mutations in early onset lethal PCa. This aggressive subset of disease requires further studying to better characterize the underlying clinical/genomic factors driving this disease.

PD48-06 DETECTION OF GERMLINE MUTATIONS IN LOCALIZED AND METASTATIC PROSTATE CANCER THROUGH GUIDLINE-BASED TESTING

You have accessJournal of UrologyProstate Cancer: Detection & Screening V (PD48)1 Apr 2020PD48-06 DETECTION OF GERMLINE MUTATIONS IN LOCALIZED AND METASTATIC PROSTATE CANCER THROUGH GUIDLINE-BASED TESTING Randy Vince*, Jake Quarles, Michelle Jacobs, Mallory Luke, Samuel Kaffenberger, Simpa Salami, Sanjay Das, Marissa Solorzano, Elena Stoffel, Sofia Merajver, Jason Hafron, and Todd Morgan Randy Vince*Randy Vince* More articles by this author , Jake QuarlesJake Quarles More articles by this author , Michelle JacobsMichelle Jacobs More articles by this author , Mallory LukeMallory Luke More articles by this author , Samuel KaffenbergerSamuel Kaffenberger More articles by this author , Simpa SalamiSimpa Salami More articles by this author , Sanjay DasSanjay Das More articles by this author , Marissa SolorzanoMarissa Solorzano More articles by this author , Elena StoffelElena Stoffel More articles by this author , Sofia MerajverSofia Merajver More articles by this author , Jason HafronJason Hafron More articles by this author , and Todd MorganTodd Morgan More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000000942.06AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: There continues to be increasing awareness that men with prostate cancer (PCa) frequently harbor germline mutations that may carry important implications for targeted therapies, mutation carriers within family members, and hereditary cancer syndromes. Most studies have focused on mutation rates in men with metastatic disease, and there is little prospective data surrounding mutation rates in men undergoing testing in clinical practice. Here, we sought to compare germline mutation rates in metastatic and localized PCa patients undergoing clinical testing. METHODS: Between 2017 – 2019 men diagnosed with PCa at Michigan Medicine and Michigan Institute of Urology (MIU) were offered multi-gene panel testing in accordance with NCCN BRCA-Related Breast and/or Ovarian Cancer Syndrome (HBOC) guidelines. Patient data was tracked in a prospectively collected registry, and rates of pathogenic/likely pathogenic mutations and variants of uncertain significance (VUS) were compared according to patient demographic and disease characteristics. RESULTS: Overall, 299 patients underwent testing, including 150 men with metastatic PCa and 149 with localized PCa. Median age was 69 (39-98) and 92% of patients were Caucasian. Rates of pathogenic/likely pathogenic germline mutations were 5.3% in metastatic and 11.4% in localized PCa patients. The most common mutations were in CHEK2 (44%), ATM (12%) and BRCA2 (12%) and FANCA (8%). CONCLUSIONS: A large proportion of men with PCa have mutations in key DNA damage repair genes. More data is needed to develop optimal screening guidelines in localized disease; however, the high detection rate in this cohort supports the current approach of offering testing based on NCCN guidelines. Source of Funding: n/a © 2020 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 203Issue Supplement 4April 2020Page: e995-e996 Advertisement Copyright & Permissions© 2020 by American Urological Association Education and Research, Inc.MetricsAuthor Information Randy Vince* More articles by this author Jake Quarles More articles by this author Michelle Jacobs More articles by this author Mallory Luke More articles by this author Samuel Kaffenberger More articles by this author Simpa Salami More articles by this author Sanjay Das More articles by this author Marissa Solorzano More articles by this author Elena Stoffel More articles by this author Sofia Merajver More articles by this author Jason Hafron More articles by this author Todd Morgan More articles by this author Expand All Advertisement PDF downloadLoading ...

The frequency of PTEN germline mutations in Chinese breast cancer patients: The PTEN gene may not be closely associated with breast cancer in the Chinese population.

PTEN is a tumour suppressor gene that has been proven to be related to breast cancer incidence and tumour progression. The aim of this study was to investigate the frequency of PTEN mutations in breast carcinomas in China and the relationships of PTEN mutations with clinicopathological parameters and clinical outcomes. Trimmomatic, Burrows-Wheeler Aligner (BWA), ANNOVAR, SAMtools, and Sanger sequencing were used to analyse PTEN mutations and identify variants in Chinese breast cancer. The frequency of PTEN mutations and the relationships of PTEN mutations with clinicopathological parameters and clinical outcomes were evaluated in breast carcinomas in China. The rate of PTEN germline mutation was 0.23% (n=9) among 3955 unselected primary breast cancer patients. Of these 9 patients, 2 carried pathogenic mutations, and both were identified as having infiltrative carcinoma. One patient had a family history. The other 7 patients carried only PTEN germline variants that were not identified as pathogenic mutations. We studied the frequency of PTEN germline mutations in a sequential cohort of Chinese breast carcinoma patients. Based on these data, we hypothesize that the germline mutation of the PTEN gene is not closely related to the occurrence of breast cancer in the Chinese population. In the clinic, the PTEN germline mutation cannot be used as the basis for the detection of breast cancer.

Nucleosome positioning stability is a modulator of germline mutation rate variation across the human genome

Nucleosome organization has been suggested to affect local mutation rates in the genome. However, the lack of de novo mutation and high-resolution nucleosome data has limited the investigation of this hypothesis. Additionally, analyses using indirect mutation rate measurements have yielded contradictory and potentially confounding results. Here, we combine data on >300,000 human de novo mutations with high-resolution nucleosome maps and find substantially elevated mutation rates around translationally stable (‘strong’) nucleosomes. We show that the mutational mechanisms affected by strong nucleosomes are low-fidelity replication, insufficient mismatch repair and increased double-strand breaks. Strong nucleosomes preferentially locate within young SINE/LINE transposons, suggesting that when subject to increased mutation rates, transposons are then more rapidly inactivated. Depletion of strong nucleosomes in older transposons suggests frequent positioning changes during evolution. The findings have important implications for human genetics and genome evolution.

Cancer Stem Cells in Pheochromocytoma and Paraganglioma.

Pheochromocytoma (PCC) and paraganglioma (PGL) are rare neuroendocrine tumors associated with high cardiovascular morbidity and variable risk of malignancy. The current therapy of choice is surgical resection. Nevertheless, PCCs/PGLs are associated with a lifelong risk of tumor persistence or recurrence. A high rate of germline or somatic mutations in numerous genes has been found in these tumors. For some, the tumorigenic processes are initiated during embryogenesis. Such tumors carry gene mutations leading to pseudohypoxic phenotypes and show more immature characteristics than other chromaffin cell tumors; they are also often multifocal or metastatic and occur at an early age, often during childhood. Cancer stem cells (CSCs) are cells with an inherent ability of self-renewal, de-differentiation, and capacity to initiate and maintain malignant tumor growth. Targeting CSCs to inhibit cancer progression has become an attractive anti-cancer therapeutic strategy. Despite progress for this strategy for solid tumors such as neuroblastoma, brain, breast, and colon cancers, no substantial advance has been made employing similar strategies in PCCs/PGLs. In the current review, we discuss findings related to the identification of normal chromaffin stem cells and CSCs, pathways involved in regulating the development of CSCs, and the importance of the stem cell niche in development and maintenance of CSCs in PCCs/PGLs. Additionally, we examine the development and feasibility of novel CSC-targeted therapeutic strategies aimed at eradicating especially recurrent and metastatic tumors.

Prevalence of somatic and germline mutations of Fumarate hydratase in uterine leiomyomas from young patients.

Hereditary leiomyomatosis and renal cell cancer (HLRCC) syndrome is caused by germline mutations in the Fumarate hydratase (FH) gene. In young women, the syndrome often presents with symptomatic uterine leiomyomas, leading to myomectomy or hysterectomy. In this study, we aimed to investigate the incidence and mutational profiles of FH-negative leiomyomas from young patients, thus allowing for early identification and triage of syndromic patients for surveillance. We evaluated 153 cases of uterine leiomyomas from women aged up to 30years for loss of FH expression by tissue microarray (TMA)-based immunohistochemical staining. Mutational analysis of tumours with loss of FH was carried out by polymerase chain reaction (PCR) amplification of 10 exons within the FH gene and subsequent Sanger sequencing. The status of promoter methylation was assessed by bisulphite sequencing. Loss of FH protein expression was detected in seven (4.6%) of 153 tested uterine leiomyomas from young patients. All FH-negative leiomyomas displayed staghorn vasculature and fibrillary/neurophil-like cytoplasm. We found that six (86%) of seven FH-negative tumours detected by immunohistochemistry harboured FH mutations, 50% of which contained germline mutations. In particular, the germline mutational rate in FH gene was 2.0% (three of 153 cases). Bisulphite sequencing analysis failed to detect promoter methylation in any of the seven tumours. Our study showed a relatively high rate of FH germline mutation in FH-negative uterine leiomyomas from patients aged up to 30years. While genetic mutations confer protein expression loss, epigenetic regulation of the FH gene appears to be unrelated to this phenotype.

Simultaneous germline and somatic sequencing in ovarian carcinoma: mutation rate and impact on clinical decision-making

ObjectiveGermline and somatic BRCA1 and BRCA2 (BRCA) mutations predict treatment response in patients with epithelial ovarian, peritoneal or fallopian tube cancer (OC), yet only germline testing is routinely pursued or reimbursed at diagnosis. We report our experience with clinical testing of paired tumor and germline DNA for OC mutations. MethodsSimultaneous sequencing using the BROCA assay of DNA from paired blood and neoplastic tissue became clinically available at our institution in 2017. We retrospectively reviewed the medical records of OC cases tested from 7/2017 to 7/2018. We calculated the rates of known pathogenic germline mutations and actionable somatic mutations, defined as those for which targeted therapies exist. ResultsWe identified 43 women (36 new diagnoses, seven recurrences) who underwent testing. Average age at diagnosis was 60. OC samples came from surgical specimens in 31 cases (72.1%), from biopsy in 11 cases (25.6%), and from cytology in one case (2.3%). We identified pathogenic germline mutations in six cases (14%), actionable somatic mutations in 15 cases (35%), and both a somatic and germline mutation in one case (2%). BRCA mutations accounted for 59% of all mutations. Of 40 cases with sufficient follow-up, providers documented reviewing results of genetic testing in 34 (85%), which influenced clinical decisions in 12 (30%). ConclusionsSimultaneous germline and tumor sequencing is an efficient way to provide enhanced information to guide the care of OC patients. This approach can identify somatic BRCA mutations at diagnosis, allowing physicians to provide PARP inhibitor maintenance and improve outcomes for those patients.

154P - Genetic characteristics of participants in the Australian Pancreatic Screening Study

BackgroundThe Australian Pancreatic Screening study offers endoscopic ultrasound surveillance for individuals at increased risk of developing pancreatic cancer. Given 5-10% of pancreatic cancers are linked to genetic predisposition, all participants are required to undergo genetic counselling. We report on the genetic characteristics of this initial cohort from our institution. MethodsThis is a multicentre, prospective cohort study. Individuals with 2 or more family members with pancreatic cancer (including one of first-degree association) and/or those with a known genetic syndrome were defined as high-risk and eligible for study entry. Subjects aged between 40 and 80 years (or 10 years younger than the relative with pancreatic cancer) were included. The study was approved by the Austin Health Human Research Ethics Committee and the first participant consented in July 2013. Data was collected through participant completed questionnaires and review of medical records. All participants were seen by a Familial Cancer Clinic. Those with an indication for further genetic testing were offered gene panel tests. Indications that there may be an inherited predisposition to pancreatic cancer includes; a family history of breast and ovarian cancer, bowel cancer, melanoma, and chronic pancreatitis. Results121 participants were recruited from 96 families. In 12 out of 96 families there was a previously known high-risk germline mutation (6 BRCA2, 3 CDKN2A, 2 PALB2 and 1 STK11). 12 out of 84 families with no known mutation were offered genetic testing, either clinic or self-funded and 8 proceeded. Germline pathogenic mutations (Class 4 or 5) were detected in 3/8 families (37.5%), making the overall pick-up rate 3/84 (3.6%). Two families had a BRCA2 mutation and the other a CDKN2A mutation. In one family, where a pathogenic BRCA2 gene mutation was identified, cascade testing identified a further 3 relatives who carried the BRCA2 mutation. The CDKN2A carrier had a significant personal and family history of cutaneous melanoma. 1 participant had a PALB2 variant of uncertain significance. ConclusionsIn an enriched population, based on pedigree and increased genetic susceptibility, the rate of germ line mutations was high. Gene panels should be considered in selected patients undergoing high risk screening. Legal entity responsible for the studyThe authors. FundingNational Health and Medical Research Council. DisclosureAll authors have declared no conflicts of interest.

Pedigree-based estimation of human mobile element retrotransposition rates.

Germline mutation rates in humans have been estimated for a variety of mutation types, including single-nucleotide and large structural variants. Here, we directly measure the germline retrotransposition rate for the three active retrotransposon elements: L1, Alu, and SVA. We used three tools for calling mobile element insertions (MEIs) (MELT, RUFUS, and TranSurVeyor) on blood-derived whole-genome sequence (WGS) data from 599 CEPH individuals, comprising 33 three-generation pedigrees. We identified 26 de novo MEIs in 437 births. The retrotransposition rate estimates for Alu elements, one in 40 births, is roughly half the rate estimated using phylogenetic analyses, a difference in magnitude similar to that observed for single-nucleotide variants. The L1 retrotransposition rate is one in 63 births and is within range of previous estimates (1:20–1:200 births). The SVA retrotransposition rate, one in 63 births, is much higher than the previous estimate of one in 900 births. Our large, three-generation pedigrees allowed us to assess parent-of-origin effects and the timing of insertion events in either gametogenesis or early embryonic development. We find a statistically significant paternal bias in Alu retrotransposition. Our study represents the first in-depth analysis of the rate and dynamics of human retrotransposition from WGS data in three-generation human pedigrees.