bims-lifras Biomed News
on Li-Fraumeni syndrome
Issue of 2020‒08‒23
eleven papers selected by
Joanna Zawacka-Pankau
University of Warsaw


  1. Genome Res. 2020 Aug 18.
    Gao F, Pan X, Dodd-Eaton EB, Recio CV, Montierth MD, Bojadzieva J, Mai PL, Zelley K, Johnson VE, Braun D, Nichols KE, Garber JE, Savage SA, Strong LC, Wang W.
      De novo mutations (DNMs) are increasingly recognized as rare disease causal factors. Identifying DNM carriers will allow researchers to study the likely distinct molecular mechanisms of DNMs. We developed Famdenovo to predict DNM status (DNM or familial mutation [FM]) of deleterious autosomal dominant germline mutations for any syndrome. We introduce Famdenovo.TP53 for Li-Fraumeni syndrome (LFS) and analyze 324 LFS family pedigrees from four US cohorts: a validation set of 186 pedigrees and a discovery set of 138 pedigrees. The concordance index for Famdenovo.TP53 prediction was 0.95 (95% CI: [0.92, 0.98]). Forty individuals (95% CI: [30, 50]) were predicted as DNM carriers, increasing the total number from 42 to 82. We compared clinical and biological features of FM versus DNM carriers: (1) cancer and mutation spectra along with parental ages were similarly distributed; (2) ascertainment criteria like early-onset breast cancer (age 20-35 yr) provides a condition for an unbiased estimate of the DNM rate: 48% (23 DNMs vs. 25 FMs); and (3) hotspot mutation R248W was not observed in DNMs, although it was as prevalent as hotspot mutation R248Q in FMs. Furthermore, we introduce Famdenovo.BRCA for hereditary breast and ovarian cancer syndrome and apply it to a small set of family data from the Cancer Genetics Network. In summary, we introduce a novel statistical approach to systematically evaluate deleterious DNMs in inherited cancer syndromes. Our approach may serve as a foundation for future studies evaluating how new deleterious mutations can be established in the germline, such as those in TP53.
    DOI:  https://doi.org/10.1101/gr.249599.119
  2. Dig Liver Dis. 2020 Aug 17. pii: S1590-8658(20)30386-8. [Epub ahead of print]
    Capurso G, Paiella S, Carrara S, Butturini G, Secchettin E, Frulloni L, Zerbi A, Falconi M.
      Pancreatic cancer is one of the main causes of cancer-related death worldwide, with a survival rate around 9%. In Italy 13,500 new cases of pancreatic cancer occurred in 2019. It is estimated that at least 5% have a hereditary background. Surveillance is advisable for healthy individuals with specific genetic syndromes with or without family history of pancreatic cancer or members of families with multiple cases of pancreatic cancer, irrespective of genetic syndromes. In 2010 the Italian Association for the Study of the Pancreas (AISP) defined criteria to include individuals in such surveillance programs with the first-round results published in 2019. In order to include other categories at high-risk and increase the diagnostic yield of surveillance, these criteria have recently been modified. The present position paper presents the updated criteria of the Italian Registry of Families at Risk of Pancreatic Cancer (IRFARPC) with their diagnostic yield calculation. Also, AISP priority projects concerning: (a) increasing awareness of citizens and primary care physicians through a dedicated App; (b) increasing access to germline testing to personalize surveillance; (c) measuring psychological impact of surveillance; (d) investigating the role of risk-modifiers and (e) evaluating the cost-effectiveness and ability to save lives of the program are briefly presented.
    Keywords:  Familial; High-risk individuals; Italy; Pancreatic cancer; Surveillance
    DOI:  https://doi.org/10.1016/j.dld.2020.07.027
  3. Future Oncol. 2020 Aug 17.
    Verdaguer H, Acosta D, Macarulla T.
      Pancreatic cancer has a poor prognosis. Focused efforts in the development of novel treatments of this disease have led to the approval of new combinations. Improvements in knowledge of the biology of these tumors have been made, and it is now widely accepted that a proportion of patients have potentially targetable altered genes. One such gene is BRCA, which confers sensibility to PARP inhibitors. Olaparib, an oral PARP inhibitor, initially demonstrated activity in Phase II clinical trials including germline BRCA-mutated patients. This was confirmed in a Phase III clinical trial in pancreatic cancer patients with a germline BRCA mutation. After the results of this study, new scenarios have been evoked. We review the development of olaparib in pancreatic cancer.
    Keywords:  BRCA mutation; DNA damage repair; PARP inhibition; biomarker; olaparib; pancreatic cancer
    DOI:  https://doi.org/10.2217/fon-2020-0334
  4. Surgery. 2020 Aug 18. pii: S0039-6060(20)30433-5. [Epub ahead of print]
    Krepline AN, Geurts JL, George B, Kamgar M, Madhavan S, Erickson BA, Hall WA, Griffin MO, Evans DB, Tsai S, Kim RY.
      BACKGROUND: Historically, germline testing of patients with pancreatic cancer was performed selectively in patients with a strong family history of cancer. Current guidelines recommend universal testing because some patients may have actionable germline pathogenic variants without family history.METHODS: We conducted a cost-effectiveness analysis using a decision-tree model to compare universal versus selective testing strategies for patients with pancreatic cancer. Costs, probabilities, and overall survival were estimated from the published literature and institutional data. One-way and probabilistic sensitivity analyses explored model uncertainty.
    RESULTS: Universal germline genetic testing had an incremental cost of $310 with an increase of 0.003 life-years. The incremental cost-effectiveness ratio was $121,924/life-years. Parameters which were most impactful (sensitivity analysis) included the median overall survival of patients with advanced disease treated with personalized therapy, cost of personalized therapy for advanced disease, and the probability of receiving personalized therapy in advanced disease. A strategy of selective testing was more cost-effective in 59% of iterations when the willingness-to-pay threshold was set to $100,000/life-years.
    CONCLUSION: Our model suggested that selective germline testing of patients with newly diagnosed pancreatic cancer is more cost-effective than universal testing. Additional research is needed to explore the impact of cascade testing of relatives on cost-effectiveness.
    DOI:  https://doi.org/10.1016/j.surg.2020.06.038
  5. Genes (Basel). 2020 Aug 12. pii: E925. [Epub ahead of print]11(8):
    Foglietta J, Ludovini V, Bianconi F, Pistola L, Reda MS, Al-Refaie A, Tofanetti FR, Mosconi A, Minenza E, Anastasi P, Molica C, Stracci F, Roila F.
      Hereditary breast and ovarian cancers are mainly linked to variants in BRCA1/2 genes. Recently, data has shown that identification of BRCA variants has an immediate impact not only in cancer prevention but also in targeted therapeutic approaches. This prospective observational study characterized the overall germline BRCA variant and variant of uncertain significance (VUS) frequency and spectrum in individuals affected by breast (BC) or ovarian cancer (OC) and in healthy individuals at risk by sequencing the entire BRCA genes. Of the 363 probands analyzed, 50 (13.8%) were BRCA1/2 mutated, 28 (7.7%) at BRCA1 and 23 (6.3%) at BRCA2 gene. The variant c.5266dupC p.(Gln1756Profs) was the most frequent alteration, representing 21.4% of the BRCA1 variants and 12.0% of all variants identified. The variant c.6313delA p.(Ile2105Tyrfs) of BRCA2 was the most frequent alteration observed in 6 patients. Interestingly, two new variants were identified in BRCA2. In addition, 25 different VUS were identified; two were reported for the first time in BRCA1 and two in BRCA2. The number of triple-negative BCs was significantly higher in patients with the pathogenic BRCA1/2-variant (36.4%) than in BRCA1/2 VUS (16.0%) and BRCA1/2 wild-type patients (10.7%) (p < 0.001). Our study reveals that the overall frequency of BRCA germline variants in the selected high-risk Italian population is about 13.8%. We believe that our results could have significant implications for preventive strategies for unaffected BRCA-carriers and effective targeted treatments such as PARP inhibitors for patients with BC or OC.
    Keywords:  BRCA1/2 variant carrier; VUS; breast cancer; genetic testing; risk evaluation
    DOI:  https://doi.org/10.3390/genes11080925
  6. BMC Med Genet. 2020 Aug 17. 21(1): 161
    Macklin-Mantia SK, Hines SL, Chaichana KL, Donaldson AM, Ko SL, Zhai Q, Samadder NJ, Riegert-Johnson DL.
      BACKGROUND: Pathogenic AXIN2 variants cause absence of permanent teeth (hypodontia), sparse hair and eye brows (ectodermal dysplasia), and gastrointestinal polyps and cancer. Inheritance is autosomal dominant with variable penetrance. Only twenty- five patients have been reported from five families. A Mayo Clinic pilot program tested 3009 newly diagnosed cancer patients for pathogenic germline variants in 83 hereditary cancer genes, including AXIN2. We found only one patient with a pathogenic AXIN2 variant.CASE PRESENTATION: The proband was a 49 year-old female who came to Otolaryngology clinic complaining of right-sided nasal obstruction. Biopsy of identified nasal polyp revealed olfactory neuroblastoma (esthesioneuroblastoma). Surgical resection with gross, total tumor resection was followed by radiation therapy. The patient enrolled in a clinical pilot of genetic testing and a pathogenic variant in AXIN2, c.1822del (p.Leu608Phefs*81) (NM_004655.3) was found. She was seen in Medical Genetics clinic and found to have a personal history of hypodontia. Her eyebrows, hair, and nails were all normal. She underwent upper endoscopy and colonoscopy. A four mm gastric adenoma was found and removed.
    CONCLUSIONS: This is the first case reported on a patient with a pathogenic, germline AXIN2 variant and an olfactory neuroblastoma or a gastric adenoma. We propose that these could be features of the AXIN2 phenotype. The known association between gastric adenomas and familial adenomatous polyposis, the other Wnt/beta-catenin disorder, supports the hypothesis that pathogenic AXIN2 variants increase risk as well. As the odds of a chance co-occurrence of a pathogenic AXIN2 variant and an olfactory neuroblastoma are so rare, it is worth exploring potential causation. We are building a clinical registry to expand understanding of the AXIN2 phenotype and request any clinicians caring for patients with pathogenic AXIN2 variants to contact us.
    Keywords:  AXIN2; Gastric adenomas; Hereditary cancer syndrome; Hereditary colorectal cancer; Hereditary polyposis; Hypodontia; Olfactory neuroblastoma
    DOI:  https://doi.org/10.1186/s12881-020-01103-0
  7. Cancers (Basel). 2020 Aug 17. pii: E2321. [Epub ahead of print]12(8):
    Rogoża-Janiszewska E, Malińska K, Cybulski C, Jakubowska A, Gronwald J, Huzarski T, Lener M, Górski B, Kluźniak W, Rudnicka H, Akbari MR, Kashyap A, Narod SA, Lubiński J, Dębniak T, On Behalf Of The Polish Hereditary Breast Cancer Consortium .
      There are twenty recurrent mutations in six breast-cancer-predisposing genes in Poland (BRCA1, BRCA2, CHEK2, PALB2, NBN, and RECQL). The frequencies of the twenty alleles have not been measured in a large series of early-onset breast cancer patients from Poland unselected for family history. We genotyped 2464 women with breast cancer diagnosed below age 41 years for twenty recurrent germline mutations in six genes, including BRCA1, BRCA2 CHEK2, PALB2, NBN, and RECQL. A mutation in one of the six genes was identified in 419 of the 2464 early-onset breast cancer cases (17%), including 22.4% of those cases diagnosed below age 31. The mutation frequency was 18.8% for familial breast cancer cases and 6% for non-familial cases. Among women with breast cancer below age 31, the mutation frequency was 23.6% for familial cases and 17.4% in non-familial cases. The majority of mutations (76.2%) were seen in BRCA1 and BRCA2. In Poland, a panel of twenty recurrent mutations in six genes can identify a genetic basis for a high percentage of early-onset cases and testing is recommended for all women with breast cancer at age 40 or below.
    Keywords:  BRCA1; BRCA2; CHEK2; NBN; PALB2; RECQL; breast cancer; hereditary
    DOI:  https://doi.org/10.3390/cancers12082321
  8. Genet Med. 2020 Aug 18.
    Roloff GW, Godley LA, Drazer MW.
      PURPOSE: To determine the degree of testing consistency among commercially available diagnostic assays for hereditary hematopoietic malignancies (HHMs).METHODS: Next-generation sequencing assays designed for the diagnosis of HHMs were studied to determine which genes were sequenced, their ability to detect variant types relevant for HHMs, and clinical-grade characteristics such as price, turnaround time, and tissue types accepted.
    RESULTS: Commercial assays varied in price (USD 250-4702), number of genes sequenced (12-73), and average turnaround time (14-42 days). A number of nongermline tissue types were accepted despite the tests being designed for germline diagnostic purposes. Multiple genes with well-characterized roles in HHM pathogenesis were omitted from more than one-third of panels intended for the evaluation of HHMs. Only 4 of 82 genes were consistently covered across all HHM diagnostic panels. The assays were highly variable in their sensitivity for structural alterations relevant to HHMs, such as copy-number variants.
    CONCLUSION: A high degree of diagnostic heterogeneity exists among commercially available HHM diagnostic assays. Many of these assays are incapable of detecting the full spectrum of HHM-associated variants, leaving patients vulnerable to the consequences of underdiagnosis, missed opportunities for screening, and the potential for donor-derived malignancies.
    Keywords:  cancer risk; germline; hematopoietic malignancies; inherited leukemia; panel testing
    DOI:  https://doi.org/10.1038/s41436-020-0934-y
  9. Semin Cancer Biol. 2020 Aug 17. pii: S1044-579X(20)30174-7. [Epub ahead of print]
    Gentiluomo M, Canzian F, Nicolini A, Gemignani F, Landi S, Campa D.
      Pancreatic cancer (PC), particularly its most common form, pancreatic ductal adenocarcinoma (PDAC), is relatively rare but highly lethal. Knowledge about PC risk factors could in the long term contribute to early diagnosis and mortality reduction. We review the current status of research on germline genetic factors for PC risk. Genome-wide association studies (GWAS) successfully identified common loci convincingly associated with PC risk, an endeavor that is still ongoing. The function of only a handful of risk loci has being thoroughly characterized so far. Secondary analyses of existing GWAS data are being used to discover novel loci. GWAS data have also been used to study additional risk factors with a Mendelian randomization approach. Polygenic/multifactorial risk scores show much larger risks than individual variants, but their use for risk stratification in the population is not warranted yet. At the other end of the spectrum of inherited PC risk factors, rare high-penetrance variants co-segregating with the disease have been observed in familial cancer syndromes that include PC, or in families with multiple recurrence of PC alone. Rare variants predicted to have a deleterious effect on function are studied also with a case-control approach, by resequencing candidate genes or whole-exomes/whole-genomes. Telomere length and mitochondrial DNA copy number are useful additional DNA-based markers of PC susceptibility. The role of common variants in prognosis of PC patients has also been explored, albeit with more limited success than risk. Finally, genetics of pancreatic neuroendocrine tumors (PNET), a rarer and heterogeneous form of PC, is still understudied.
    Keywords:  Pancreatic cancer; cancer prognosis; cancer risk factors; cancer susceptibility; genetic polymorphisms
    DOI:  https://doi.org/10.1016/j.semcancer.2020.08.003
  10. Ophthalmic Genet. 2020 Aug 17. 1-7
    Xu L, Shen L, Polski A, Prabakar RK, Shah R, Jubran R, Kim JW, Biegel J, Kuhn P, Cobrinik D, Hicks J, Gai X, Berry JL.
      BACKGROUND: Detection of germline RB1 mutations is critical for risk assessment of retinoblastoma (RB) patients. Assessment of somatic copy number alterations (SCNAs) is also critically important because of their prognostic significance. Herein we present a refined approach for the simultaneous identification of RB1 variants and SCNAs in the aqueous humor (AH) of RB eyes.MATERIALS AND METHODS: Subjects included 7 eyes of 6 RB patients that underwent AH extraction, and 4 matched tumor samples. Cell-free DNA (cfDNA) was isolated and sequenced to assess genome-wide SCNAs. The same sequencing libraries then underwent targeted resequencing and mutation detection using a custom hybridization panel that targets RB1 and MYCN. Illumina paired-end 2x150bp sequencing was used to characterize single-nucleotide variants (SNVs) and loss of heterozygosity (LOH). Results were compared to peripheral blood RB1 testing. Tumor fraction (TFx) was calculated using ichorCNA.
    RESULTS: Four of 7 AH samples contained clinically significant SCNAs. Of the 3 other samples, 1 showed focal MYCN amplification and 1 showed focal RB1 deletion. All 4 enucleated tumors contained SCNAs. Mutational analysis of tumor DNA identified all first hits (2 germline RB1 SNVs, 2 germline CNAs) and second hits (4 RB1 SNVs). RB1 variants in AH were concordant with those obtained from corresponding tumor tissue and blood. In AH samples without paired tumor, both RB1 hits were identified with high variant allele frequency, even in the absence of SCNAs.
    CONCLUSIONS: AH liquid biopsy is a minimally invasive, in vivo alternative to tissue analysis for the simultaneous identification of RB1 variants and SCNAs in RB eyes.
    Keywords:   RB1 gene; Aqueous humor; mutational analysis; retinoblastoma; somatic copy number alterations
    DOI:  https://doi.org/10.1080/13816810.2020.1799417