bims-lifras Biomed News
on Li-Fraumeni syndrome
Issue of 2020–02–23
eleven papers selected by
Joanna Zawacka-Pankau
  1. The spectrum of BRCA1 and BRCA2 mutations and clinicopathological characteristics in Chinese women with early-onset breast cancer.
  2. Adjuvant radiotherapy induces secondary tumor events in breast cancer patients with Li-Fraumeni syndrome.
  3. Germline mutation in 1,338 BRCA-negative Chinese hereditary breast and/or ovarian cancer patients: clinical testing with a multigene test panel.
  4. Clinical applications of polygenic breast cancer risk: a critical review and perspectives of an emerging field.
  5. Whole Exome Sequencing Identifies Candidate Genes Associated with Hereditary Predisposition to Uveal Melanoma.
  6. Functional Characterization of a Missense Variant of MLH1 Identified in Lynch Syndrome Pedigree.
  7. Clinical characteristics and outcomes of SDHB-related pheochromocytoma and paraganglioma in children and adolescents.
  8. Easy One-Step Amplification and Labeling Procedure for Copy Number Variation Detection.
  9. Inherited DNA-repair gene mutations in African American men with prostate cancer.
  10. Germline and Somatic Tumor Testing in Epithelial Ovarian Cancer: ASCO Guideline Summary.
  11. Geographic and Ethnic Heterogeneity of Germline BRCA1 or BRCA2 Mutation Prevalence Among Patients With Metastatic Pancreatic Cancer Screened for Entry Into the POLO Trial.
  1. Breast Cancer Res Treat. 2020 Feb 18.
    The spectrum of BRCA1 and BRCA2 mutations and clinicopathological characteristics in Chinese women with early-onset breast cancer.
    Lili Chen, Fangmeng Fu, Meng Huang, Jinxing Lv, Wenzhe Zhang, Chuan Wang.
       PURPOSE: BRCA1/2 mutations represent a high risk of breast cancer and are related to early-onset breast cancer. However, few studies have reported the relationship between BRCA1/2 mutations and their clinical characteristics in early-onset breast cancers. This study is the first article that characterizes the risk factor profiles in Chinese patients selected by the age of onset (≤ 40 years old). We found some differences in the prevalence of germline BRCA1/2 mutations between Asian and Western countries.
    METHODS: A total of 1371 consecutive unselected Chinese early-onset breast cancer patients were enrolled from the Fujian Medical University Union Hospital, China, and screened for germline BRCA1/2 mutations. Full-exome sequencing in next-generation sequencing technology was performed in all patients to examine BRCA1/2 mutations.
    RESULTS: In our study, 25 (1.8%) and 61 (4.4%) patients were identified with BRCA1 and BRCA2 mutations, respectively, among the unselected early-onset breast cancer patients. BRCA1 mutations were associated with pregnancies (p = 0.026), and BRCA1 carriers had a higher likelihood of being HR positive (p < 0.001), HER2 negative (p < 0.001), or high grade (p = 0.002) than noncarriers. Among BRCA2 mutations, the age of onset was younger in carriers than in noncarriers (p = 0.017), and BRCA2 carriers were more likely to have lymph node metastasis (p = 0.004). HR-positive or HER2-negative patients were likely to be positive for BRCA2 mutations (p < 0.001). Overall, 14 BRCA1 mutations and 8 BRCA2 mutations were first reported in our study CONCLUSION: This study provided some information about the spectrum of BRCA1/2 mutations and characterized the risk factors for early-onset breast cancer in China.
    Keywords:  BRCA1/2; Breast neoplasms; Chinese; Germline mutations; Prevalence
    DOI:  https://doi.org/10.1007/s10549-020-05573-x
  2. Ann Oncol. 2019 May;pii: S0923-7534(19)30364-3. [Epub ahead of print]30 Suppl 3 iii30
    Adjuvant radiotherapy induces secondary tumor events in breast cancer patients with Li-Fraumeni syndrome.
    K Rounis, T Koukaki, C Christodoulou, C Papadimitriou, D Tryfonopoulos, D Mavroudis, S Aggelaki, F Fostira, E Saloustros.
      
    DOI:  https://doi.org/10.1093/annonc/mdz096.010
  3. J Mol Diagn. 2020 Feb 14. pii: S1525-1578(20)30036-2. [Epub ahead of print]
    Germline mutation in 1,338 BRCA-negative Chinese hereditary breast and/or ovarian cancer patients: clinical testing with a multigene test panel.
    Ava Kwong, Vivian Yvonne Shin, Jiawei Chen, Isabella Wai-Yin Cheuk, Cecilia Ys Ho, Chun Hang Au, Karen K L Chan, Hextan Y S Ngan, Tsun Leung Chan, James M Ford, Edmond Sk Ma.
      Differences in the mutation spectrum across ethnicities suggest that it is important to identify genes in addition to common high penetrant genes to estimate the associated breast cancer risk in Chinese. 1,338 high-risk breast cancer patients who tested negative for germline BRCA1, BRCA2, TP53 and PTEN mutations between 2007-2017 were selected from the Hong Kong Hereditary Breast Cancer Family Registry. Patient samples were subjected to next-generation DNA sequencing using a multigene panel (Color Genomics). All detected pathogenic variants were validated by bi-directional DNA sequencing. The sequencing data was co-analyzed by our in-house developed bioinformatics pipeline. Sixty-one pathogenic variants (4.6%) were identified in this cohort in 11 cancer predisposition genes. The majority of the carriers (77.1%) had early-onset of breast cancer (age <45), 32.8% had family members with breast cancer and 11.5% had triple-negative breast cancer (TNBC). The most common mutated genes were PALB2 (1.4%), RAD51D (0.8%) and ATM (0.8%). A total of 612 variants of unknown significance (VUS) were identified in 494 patients, and 87.4% of the VUS were missense mutations. Pathogenic variants in cancer predisposition genes beyond BRCA1, BRCA2, TP53 and PTEN were detected in an additional 4.6% of the patients using the multigene test panel. PALB2 (1.4%) and RAD51D (0.8%) were the most commonly mutated genes in patients who tested mutation-negative by a 4-gene panel.
    DOI:  https://doi.org/10.1016/j.jmoldx.2020.01.013
  4. Breast Cancer Res. 2020 Feb 17. 22(1): 21
    Clinical applications of polygenic breast cancer risk: a critical review and perspectives of an emerging field.
    Tatiane Yanes, Mary-Anne Young, Bettina Meiser, Paul A James.
      Polygenic factors are estimated to account for an additional 18% of the familial relative risk of breast cancer, with those at the highest level of polygenic risk distribution having a least a twofold increased risk of the disease. Polygenic testing promises to revolutionize health services by providing personalized risk assessments to women at high-risk of breast cancer and within population breast screening programs. However, implementation of polygenic testing needs to be considered in light of its current limitations, such as limited risk prediction for women of non-European ancestry. This article aims to provide a comprehensive review of the evidence for polygenic breast cancer risk, including the discovery of variants associated with breast cancer at the genome-wide level of significance and the use of polygenic risk scores to estimate breast cancer risk. We also review the different applications of this technology including testing of women from high-risk breast cancer families with uninformative genetic testing results, as a moderator of monogenic risk, and for population screening programs. Finally, a potential framework for introducing testing for polygenic risk in familial cancer clinics and the potential challenges with implementing this technology in clinical practice are discussed.
    Keywords:  Breast cancer; Polygenic risk score; Risk prediction
    DOI:  https://doi.org/10.1186/s13058-020-01260-3
  5. Ophthalmology. 2019 Nov 18. pii: S0161-6420(19)32274-2. [Epub ahead of print]
    Whole Exome Sequencing Identifies Candidate Genes Associated with Hereditary Predisposition to Uveal Melanoma.
    Mohamed H Abdel-Rahman, Klarke M Sample, Robert Pilarski, Tomas Walsh, Timothy Grosel, Daniel Kinnamon, Getachew Boru, James B Massengill, Lynn Schoenfield, Ben Kelly, David Gordon, Peter Johansson, Meghan J DeBenedictis, Arun Singh, Silvia Casadei, Frederick H Davidorf, Peter White, Andrew W Stacey, James Scarth, Ellie Fewings, Marc Tischkowitz, Mary-Claire King, Nicholas K Hayward, Colleen M Cebulla.
       PURPOSE: To identify susceptibility genes associated with hereditary predisposition to uveal melanoma (UM) in patients with no detectable germline BAP1 alterations.
    DESIGN: Retrospective case series from academic referral centers.
    PARTICIPANTS: Cohort of 154 UM patients with high risk of hereditary cancer defined as patients with 1 or more of the following: (1) familial UM, (2) young age (<35 years) at diagnosis, (3) personal history of other primary cancers, and (4) family history of 2 or more primary cancers with no detectable mutation or deletion in BAP1 gene.
    METHODS: Whole exome sequencing, a cancer gene panel, or both were carried out. Probands included 27 patients with familial UM, 1 patient with bilateral UM, 1 patient with congenital UM, and 125 UM patients with strong personal or family histories, or both, of cancer. Functional validation of variants was carried out by immunohistochemistry, reverse-transcriptase polymerase chain reaction, and genotyping.
    MAIN OUTCOME MEASURES: Clinical characterization of UM patients with germline alterations in known cancer genes.
    RESULTS: We identified actionable pathogenic variants in 8 known hereditary cancer predisposition genes (PALB2, MLH1, MSH6, CHEK2, SMARCE1, ATM, BRCA1, and CTNNA1) in 9 patients, including 3 of 27 patients (11%) with familial UM and 6 of 127 patients (4.7%) with a high risk for cancer. Two patients showed pathogenic variants in CHEK2 and PALB2, whereas variants in the other genes each occurred in 1 patient. Biallelic inactivation of PALB2 and MLH1 was observed in tumors from the respective patients. The frequencies of pathogenic variants in PALB2, MLH1, and SMARCE1 in UM patients were significantly higher than the observed frequencies in noncancer controls (PALB2: P = 0.02; odds ratio, 8.9; 95% confidence interval, 1.5-30.6; MLH1: P = 0.04; odds ratio, 25.4; 95% confidence interval, 1.2-143; SMARCE1: P = 0.001; odds ratio, 2047; 95% confidence interval, 52-4.5e15, respectively).
    CONCLUSIONS: The study provided moderate evidence of gene and disease association of germline mutations in PALB2 and MLH1 with hereditary predisposition to UM. It also identified several other candidate susceptibility genes. The results suggest locus heterogeneity in predisposition to UM. Genetic testing for hereditary predisposition to cancer is warranted in UM patients with strong personal or family history of cancers, or both.
    DOI:  https://doi.org/10.1016/j.ophtha.2019.11.009
  6. Dis Markers. 2020 ;2020 8360841
    Functional Characterization of a Missense Variant of MLH1 Identified in Lynch Syndrome Pedigree.
    Tahir Zaib, Chunhui Zhang, Komal Saleem, Lidan Xu, Qian Qin, Yusi Wang, Wei Ji, Hanif Khan, Hanfei Yu, Siqi Zhu, Wei Gao, Yun Huang, Xueyuan Jia, Jie Wu, Hongtao Song, Yanqiao Zhang, Wenjing Sun, Songbin Fu.
      Lynch syndrome (LS) is the most common hereditary colorectal cancer (CRCs) inherited in an autosomal-dominant manner. Here, we reported a multigeneration Chinese family clinically diagnosed with LS according to the Amsterdam II criteria. To identify the underlying causative gene for LS in this family, whole-exome sequencing (WES) was performed. A germline missense variant (c.2054C>T:p.S685F) in exon 18 of MLH1 was successfully identified by WES. Sanger sequencing verified the results of WES and also confirmed the cosegregation of the MLH1 missense variant in all affected members of the family including two unaffected family members. Bioinformatic tools predicted the identified MLH1 variant as deleterious. Immunohistochemistry (IHC) staining showed loss of MLH1 and PMS2 protein expression. In vitro expression analysis also revealed that the identified MLH1 missense variant (c.2054C>T:p.S685F) results in reduced expression of both MLH1 and PMS2 proteins. Based on the American College of Medical Genetics and Genomics (ACMG) guidelines, the missense mutation c.2054C>T in MLH1 was classified as a "pathogenic" variant. Two unaffected family members were later recommended for colonoscopy and other important cancer diagnostic inspections every 1-2 years as both were at higher risk of LS. In conclusion, our findings widen the genotypic spectrum of MLH1 mutations responsible for LS. This study increases the phenotypic spectrum of LS which will certainly help the clinicians in diagnosing LS in multigeneration families. This study also puts emphasis on the importance of genetic counselling for the benefit of asymptomatic carriers of MMR gene variants who are at higher risk of LS.
    DOI:  https://doi.org/10.1155/2020/8360841
  7. J Cancer Res Clin Oncol. 2020 Feb 15.
    Clinical characteristics and outcomes of SDHB-related pheochromocytoma and paraganglioma in children and adolescents.
    Ivana Jochmanova, April Melody T Abcede, Ruby Jane S Guerrero, Chandy Lou P Malong, Robert Wesley, Thanh Huynh, Melissa K Gonzales, Katherine I Wolf, Abhishek Jha, Marianne Knue, Tamara Prodanov, Naris Nilubol, Leilani B Mercado-Asis, Constantine A Stratakis, Karel Pacak.
       PURPOSE: Pheochromocytomas/paragangliomas (PHEOs/PGLs) are rare in children with only a few SDHB mutation-related cases. Previous studies on children were conducted in small cohorts. This large set of pediatric patients provides robust data in the evaluation of clinical outcomes.
    METHODS: Sixty-four pediatric PHEO/PGL patients with SDHB germline mutations were included in the present study. The clinical presentation, disease course, and survival rate were evaluated.
    RESULTS: Thirty-eight males and 26 females were diagnosed with PHEO/PGL at a median age of 13 years. The majority of patients displayed norepinephrine hypersecretion and 73.44% initially presented with a solitary tumor. Metastases developed in 70% of patients at the median age of 16 years and were mostly diagnosed first 2 years and in years 12-18 post-diagnosis. The presence of metastases at the time of diagnosis had a strong negative impact on survival in males but not in females. The estimated 5-, 10-, and 20-year survival rates were 100%, 97.14%, and 77.71%, respectively.
    CONCLUSION: The present report has highlighted several important aspects in the management of pediatric patients with SDHB mutations associated-PHEO/PGL. Initial diagnostic evaluation of SDHB mutation carriers should be started at age of 5-6 years with initial work-up focusing on abdominal region. Thorough follow-up is crucial first 2 years post-diagnosis and more frequent follow-ups are needed in years 10-20 post-diagnosis due to the increased risk of metastases. Although this age group developed metastasis as early as 5 years from diagnosis, we have shown that the overall 20-year prognosis and survival are good.
    Keywords:  Paraganglioma; Pediatric oncology; Pheochromocytoma; SDHB mutation
    DOI:  https://doi.org/10.1007/s00432-020-03138-5
  8. Clin Chem. 2020 Feb 18. pii: hvaa002. [Epub ahead of print]
    Easy One-Step Amplification and Labeling Procedure for Copy Number Variation Detection.
    Sebastián Blesa, María D Olivares, Andy S Alic, Alicia Serrano, Verónica Lendinez, Verónica González-Albert, Laura Olivares, Sergio Martínez-Hervás, José M Juanes, Pablo Marín, Jose T Real, Blanca Navarro, Ana B García-García, Felipe J Chaves, Carmen Ivorra.
       BACKGROUND: The specific characteristics of copy number variations (CNVs) require specific methods of detection and characterization. We developed the Easy One-Step Amplification and Labeling procedure for CNV detection (EOSAL-CNV), a new method based on proportional amplification and labeling of amplicons in 1 PCR.
    METHODS: We used tailed primers for specific amplification and a pair of labeling probes (only 1 labeled) for amplification and labeling of all amplicons in just 1 reaction. Products were loaded directly onto a capillary DNA sequencer for fragment sizing and quantification. Data obtained could be analyzed by Microsoft Excel spreadsheet or EOSAL-CNV analysis software. We developed the protocol using the LDLR (low density lipoprotein receptor) gene including 23 samples with 8 different CNVs. After optimizing the protocol, it was used for genes in the following multiplexes: BRCA1 (BRCA1 DNA repair associated), BRCA2 (BRCA2 DNA repair associated), CHEK2 (checkpoint kinase 2), MLH1 (mutL homolog 1) plus MSH6 (mutS homolog 6), MSH2 (mutS homolog 2) plus EPCAM (epithelial cell adhesion molecule) and chromosome 17 (especially the TP53 [tumor protein 53] gene). We compared our procedure with multiplex ligation-dependent probe amplification (MLPA).
    RESULTS: The simple procedure for CNV detection required 150 min, with <10 min of handwork. After analyzing >240 samples, EOSAL-CNV excluded the presence of CNVs in all controls, and in all cases, results were identical using MLPA and EOSAL-CNV. Analysis of the 17p region in tumor samples showed 100% similarity between fluorescent in situ hybridization and EOSAL-CNV.
    CONCLUSIONS: EOSAL-CNV allowed reliable, fast, easy detection and characterization of CNVs. It provides an alternative to targeted analysis methods such as MLPA.
    Keywords:  Lynch syndrome; Mutation detection system; copy number variations; familial hypercholesterolemia; genetic diagnosis; hereditary breast cancer
    DOI:  https://doi.org/10.1093/clinchem/hvaa002
  9. Oncotarget. 2020 Jan 28. 11(4): 440-442
    Inherited DNA-repair gene mutations in African American men with prostate cancer.
    Oliver Sartor, Shan Yang, Elisa Ledet, Marcus Moses, Piper Nicolosi.
      African American men with prostate cancer are understudied relative to Caucasians with prostate cancer with regard to testing for pathogenic germline DNA repair gene mutations. Herein we evaluate these two populations in a large commercial dataset and compare the detection of pathogenic/likely pathogenic alterations in 14 well annotated DNA repair genes (BRCA2, BRCA1, PALB2, ATM, RAD51C, CHEK2, PMS2, BARD1, BRIP1, MLH1, MSH2, MSH6, NBN, and RAD51D). Overall, pathogenic or likely pathogenic alterations in these 14 DNA repair genes were less likely to be detected in African Americans as compared to Caucasians. Upon a more in-depth analysis, the risk of germline pathogenic/likely pathogenic BRCA mutations was similar between the two populations whereas there was a lower risk among African Americans for the non-BRCA mutations. No African American men were noted to have mutations in BARD1, BRIP1, MLH1, MSH2, MSH6, NBN, and RAD51D in this data set. Stage, grade, and metastatic status were not assessed in this group of patients. Larger and more detailed studies conducted in men with prostate cancer are required to confirm these findings.
    Keywords:  African American; BRCA; DNA repair; ethnicity; prostate cancer
    DOI:  https://doi.org/10.18632/oncotarget.27456
  10. JCO Oncol Pract. 2020 Feb 19. JOP1900773
    Germline and Somatic Tumor Testing in Epithelial Ovarian Cancer: ASCO Guideline Summary.
    Panagiotis A Konstantinopoulos, Christina Lacchetti, Christina M Annunziata.
      
    DOI:  https://doi.org/10.1200/JOP.19.00773
  11. J Clin Oncol. 2020 Feb 19. JCO1901890
    Geographic and Ethnic Heterogeneity of Germline BRCA1 or BRCA2 Mutation Prevalence Among Patients With Metastatic Pancreatic Cancer Screened for Entry Into the POLO Trial.
    Talia Golan, Hedy L Kindler, Joon Oh Park, Michele Reni, Teresa Macarulla, Pascal Hammel, Eric Van Cutsem, Dirk Arnold, Daniel Hochhauser, David McGuinness, Gershon Y Locker, Teodora Goranova, Philipp Schatz, Yu-Zhen Liu, Michael J Hall.
       PURPOSE: Germline BRCA1 and/or BRCA2 mutations (gBRCAms) are risk factors for pancreatic cancer. The extent to which demographic and geographic factors affect the uptake of gBRCAm testing in pancreatic cancer (PC) is unknown.
    METHODS: We conducted a retrospective, descriptive analysis of demographic/geographic data from the first 2,206 patients with metastatic PC (mPC) screened for eligibility to enter the phase III POLO trial of maintenance olaparib. No formal statistical tests were performed.
    RESULTS: Of 2,167 patients with previously unknown gBRCAm status, 128 (5.9%) had a newly identified gBRCAm; rates were highest in the United States, France, and Israel (9.5%, 7.6%, and 7.4%, respectively). When including patients with a previously known gBRCAm, prevalence rose to 7.2% (or 5.8% after excluding populations enriched in Ashkenazi Jews, who are known to have a high rate of BRCA1 and BRCA2 founder mutations). Patients with a gBRCAm were slightly younger (57.9 v 61.1 years) and more likely to have early-onset mPC than those without. Higher newly identified gBRCAm prevalence was observed among African American (n = 28) versus white (n = 1,808), Asian (n = 218), and other (n = 61) patients (10.7% v 6.1%, 5.0%, and 1.6%, respectively). Of 139 white patients with a gBRCAm, 110 were newly identified during screening; the majority of gBRCAms in African American, Asian, and Hispanic patients (n = 3, n = 11, and n = 5, respectively) were newly identified.
    CONCLUSION: We identified substantial geographic and some racial variability in gBRCAm prevalence among patients with mPC, an important consideration given the increased use of familial screening and possible future use of targeted therapies in this setting. Although our study included small numbers of nonwhite patients, prior knowledge of their gBRCAm status was limited compared with their white counterparts, which suggests disparities in genetic testing uptake.
    DOI:  https://doi.org/10.1200/JCO.19.01890
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