bims-lifras Biomed News
on Li-Fraumeni syndrome
Issue of 2020–10–18
ten papers selected by
Joanna Zawacka-Pankau, University of Warsaw
  1. Identifying possible germline variants from tumor-only sequencing of hematological malignancies.
  2. The role of TP53 pathogenic variants in early-onset HER2-positive breast cancer.
  3. Identification of Germline Mutations in Melanoma Patients with Early Onset, Double Primary Tumors, or Family Cancer History by NGS Analysis of 217 Genes.
  4. Myeloid neoplasms with germline predisposition: Practical considerations and complications in the search for new susceptibility loci.
  5. Germline predisposition in myeloid neoplasms: Unique genetic and clinical features of GATA2 deficiency and SAMD9/SAMD9L syndromes.
  6. E-Cadherin (CDH1 Gene) Germline Mutations in Gastric Cancer: Evolutions and Innovations.
  7. CRISPR-Cas9/long-read sequencing approach to identify cryptic mutations in BRCA1 and other tumour suppressor genes.
  8. A germline 1;3 translocation disrupting the VHL gene: a novel genetic cause for von Hippel-Lindau.
  9. Blood functional assay for rapid clinical interpretation of germline TP53 variants.
  10. GATA2 Related Conditions and Predisposition to Pediatric Myelodysplastic Syndromes.
  1. Leuk Lymphoma. 2020 Oct 15. 1-4
    Identifying possible germline variants from tumor-only sequencing of hematological malignancies.
    Jianming Shao, Sishir Subedi, Kristi Pepper, Sabrina Badgett, Paul A Christensen, Heather L Hendrickson, Jessica S Thomas, Randall J Olsen, Zejuan Li.
      
    DOI:  https://doi.org/10.1080/10428194.2020.1832665
  2. Fam Cancer. 2020 Oct 14.
    The role of TP53 pathogenic variants in early-onset HER2-positive breast cancer.
    Carla Escudeiro, Carla Pinto, Joana Vieira, Ana Peixoto, Pedro Pinto, Manuela Pinheiro, Catarina Santos, Joana Guerra, Susana Lisboa, Rui Santos, João Silva, Conceição Leal, Nuno Coimbra, Paula Lopes, Marco Ferreira, Ana B Sousa, Manuel R Teixeira.
      Breast cancer is the most frequent event in Li-Fraumeni syndrome associated with germline TP53 variants. Some studies have shown that breast cancers in women with Li-Fraumeni syndrome are commonly HER2-positive, suggesting that HER2 amplification or over-expression in a young woman may be a useful criterion to test for germline variants in the TP53 gene. We assessed the prevalence of germline TP53 variants by Sanger sequencing or next-generation sequencing in 149 women with HER2-positive breast cancer diagnosed until age 40. The pattern of HER2 amplification was evaluated with dual-probe FISH in a subset of breast carcinomas from patients with germline TP53 variants as compared with those of noncarriers. Among 149 women tested, three presented a deleterious TP53 germline variant (2%), with one patient diagnosed at age 31 and the other two with bilateral breast cancer at ages 29/33 and 28/32, respectively. Three of the 36 patients (8.3%) with the first breast cancer diagnosed at age 31 or younger presented a pathogenic TP53 variant. Additionally, all TP53 deleterious variant carriers had a first degree relative diagnosed with different early-onset cancers (frequently not belonging to the Li-Fraumeni syndrome tumor spectrum) diagnosed at age 45 or younger. Higher levels of HER2 amplification were found in breast carcinomas of TP53 pathogenic variant carriers than in those of noncarriers. Deleterious germline TP53 variants account for a small proportion of early-onset HER2-positive breast cancers, but these seem to have higher HER2 amplification ratios. All TP53 pathogenic variant carriers found in this study had the first breast carcinoma diagnosed at age 31 or younger and a first-degree relative with early-onset cancer. Further studies are needed to clarify if HER2 status in early-onset breast cancer patients, in combination with other personal and/or familial cancer history, is useful to update the TP53 testing criteria.
    Keywords:  HER2-positive breast cancer; Li-fraumeni syndrome; Next-generation sequencing; TP53 germline variants
    DOI:  https://doi.org/10.1007/s10689-020-00212-2
  3. Biomedicines. 2020 Oct 09. pii: E404. [Epub ahead of print]8(10):
    Identification of Germline Mutations in Melanoma Patients with Early Onset, Double Primary Tumors, or Family Cancer History by NGS Analysis of 217 Genes.
    Lenka Stolarova, Sandra Jelinkova, Radka Storchova, Eva Machackova, Petra Zemankova, Michal Vocka, Ondrej Kodet, Jan Kral, Marta Cerna, Zuzana Volkova, Marketa Janatova, Jana Soukupova, Viktor Stranecky, Pavel Dundr, Lenka Foretova, Libor Macurek, Petra Kleiblova, Zdenek Kleibl.
      Cutaneous melanoma is the deadliest skin malignity with a rising prevalence worldwide. Patients carrying germline mutations in melanoma-susceptibility genes face an increased risk of melanoma and other cancers. To assess the spectrum of germline variants, we analyzed 264 Czech melanoma patients indicated for testing due to early melanoma (at <25 years) or the presence of multiple primary melanoma/melanoma and other cancer in their personal and/or family history. All patients were analyzed by panel next-generation sequencing targeting 217 genes in four groups: high-to-moderate melanoma risk genes, low melanoma risk genes, cancer syndrome genes, and other genes with an uncertain melanoma risk. Population frequencies were assessed in 1479 population-matched controls. Selected POT1 and CHEK2 variants were characterized by functional assays. Mutations in clinically relevant genes were significantly more frequent in melanoma patients than in controls (31/264; 11.7% vs. 58/1479; 3.9%; p = 2.0 × 10-6). A total of 9 patients (3.4%) carried mutations in high-to-moderate melanoma risk genes (CDKN2A, POT1, ACD) and 22 (8.3%) patients in other cancer syndrome genes (NBN, BRCA1/2, CHEK2, ATM, WRN, RB1). Mutations in high-to-moderate melanoma risk genes (OR = 52.2; 95%CI 6.6-413.1; p = 3.2 × 10-7) and in other cancer syndrome genes (OR = 2.3; 95%CI 1.4-3.8; p = 0.003) were significantly associated with melanoma risk. We found an increased potential to carry these mutations (OR = 2.9; 95%CI 1.2-6.8) in patients with double primary melanoma, melanoma and other primary cancer, but not in patients with early age at onset. The analysis revealed affected genes in Czech melanoma patients and identified individuals who may benefit from genetic testing and future surveillance management of mutation carriers.
    Keywords:  NGS; familial melanoma; germline mutations; hereditary cancer predisposition; melanoma; panel sequencing
    DOI:  https://doi.org/10.3390/biomedicines8100404
  4. Best Pract Res Clin Haematol. 2020 Sep;pii: S1521-6926(20)30052-9. [Epub ahead of print]33(3): 101191
    Myeloid neoplasms with germline predisposition: Practical considerations and complications in the search for new susceptibility loci.
    Hetty E Carraway, Thomas LaFramboise.
      Genomic research in hematological malignancies has focused far more prominently on somatic mutations than on germline variants. Although increasing numbers of germline variants are being identified, a substantial proportion of familial myeloid malignancies have no causal allele pinpointed. Here we review the biological, technological, and clinical challenges that stand in the way of the goal of establishing, implementing, and interpreting a comprehensive panel of germline variants for testing. Achieving this goal would inform care for large numbers of myeloid malignancy patients. Furthermore, knowledge of germline susceptibility variants and their corresponding genes will shed light on disease processes, potentially suggesting therapeutic strategies tailored to specific variants.
    Keywords:  Acute myeloid leukemia; Germline mutation; Myelodysplastic syndromes; Myeloid neoplasia
    DOI:  https://doi.org/10.1016/j.beha.2020.101191
  5. Best Pract Res Clin Haematol. 2020 Sep;pii: S1521-6926(20)30058-X. [Epub ahead of print]33(3): 101197
    Germline predisposition in myeloid neoplasms: Unique genetic and clinical features of GATA2 deficiency and SAMD9/SAMD9L syndromes.
    Sushree S Sahoo, Emilia J Kozyra, Marcin W Wlodarski.
      Increasing awareness about germline predisposition and the widespread application of unbiased whole exome sequencing contributed to the discovery of new clinical entities with high risk for the development of haematopoietic malignancies. The revised 2016 WHO classification introduced a novel category of "myeloid neoplasms with germline predisposition" with GATA2, CEBPA, DDX41, RUNX1, ANKRD26 and ETV6 genes expanding the spectrum of hereditary myeloid neoplasms (MN). Since then, more germline causes of MN were identified, including SAMD9, SAMD9L, and ERCC6L2. This review describes the genetic and clinical spectrum of predisposition to MN. The main focus lies in delineation of phenotypes, genetics and management of GATA2 deficiency and the novel SAMD9/SAMD9L-related disorders. Combined, GATA2 and SAMD9/SAMD9L (SAMD9/9L) syndromes are recognized as most frequent causes of primary paediatric myelodysplastic syndromes, particularly in setting of monosomy 7. To date, ~550 cases with germline GATA2 mutations, and ~130 patients with SAMD9/9L mutations had been reported in literature. GATA2 deficiency is a highly penetrant disorder with a progressive course that often rapidly necessitates bone marrow transplantation. In contrast, SAMD9/9L disorders show incomplete penetrance with various clinical outcomes ranging from spontaneous haematological remission observed in young children to malignant progression.
    Keywords:  GATA2; Germline predisposition; Hereditary MDS; SAMD9; SAMD9L
    DOI:  https://doi.org/10.1016/j.beha.2020.101197
  6. Cancers (Basel). 2020 Oct 11. pii: E2920. [Epub ahead of print]12(10):
    E-Cadherin (CDH1 Gene) Germline Mutations in Gastric Cancer: Evolutions and Innovations.
    Giovanni Corso, Bernardo Bonanni.
      Family history has contributed greatly to understanding inherited diseases throughout the centuries, in particular familial and hereditary cancer syndromes [...].
    DOI:  https://doi.org/10.3390/cancers12102920
  7. J Med Genet. 2020 Oct 15. pii: jmedgenet-2020-107320. [Epub ahead of print]
    CRISPR-Cas9/long-read sequencing approach to identify cryptic mutations in BRCA1 and other tumour suppressor genes.
    Tom Walsh, Silvia Casadei, Katherine M Munson, Mary Eng, Jessica B Mandell, Suleyman Gulsuner, Mary-Claire King.
      Current clinical approaches for mutation discovery are based on short sequence reads (100-300 bp) of exons and flanking splice sites targeted by multigene panels or whole exomes. Short-read sequencing is highly accurate for detection of single nucleotide variants, small indels and simple copy number differences but is of limited use for identifying complex insertions and deletions and other structural rearrangements. We used CRISPR-Cas9 to excise complete BRCA1 and BRCA2 genomic regions from lymphoblast cells of patients with breast cancer, then sequenced these regions with long reads (>10 000 bp) to fully characterise all non-coding regions for structural variation. In a family severely affected with early-onset bilateral breast cancer and with negative (normal) results by gene panel and exome sequencing, we identified an intronic SINE-VNTR-Alu retrotransposon insertion that led to the creation of a pseudoexon in the BRCA1 message and introduced a premature truncation. This combination of CRISPR-Cas9 excision and long-read sequencing reveals a class of complex, damaging and otherwise cryptic mutations that may be particularly frequent in tumour suppressor genes replete with intronic repeats.
    Keywords:  genetic testing; genetics; germ-line mutation; mutation; sequence analysis
    DOI:  https://doi.org/10.1136/jmedgenet-2020-107320
  8. J Med Genet. 2020 Oct 16. pii: jmedgenet-2020-107308. [Epub ahead of print]
    A germline 1;3 translocation disrupting the VHL gene: a novel genetic cause for von Hippel-Lindau.
    Christopher J Ricketts, Cathy D Vocke, Martin Lang, Xiongfong Chen, Yongmei Zhao, Bao Tran, Mayank Tandon, Laura S Schmidt, Mark W Ball, W Marston Linehan.
      Von Hippel-Lindau (VHL) disease is an autosomal dominant hereditary tumour susceptibility disease caused by germline pathogenic variation of the VHL tumour suppressor gene. Affected individuals are at risk of developing multiple malignant and benign tumours in a number of organs.In this report, a male patient in his 20s who presented to the Urologic Oncology Branch at the National Cancer Institute with a clinical diagnosis of VHL was found to have multiple cerebellar haemangioblastomas, bilateral epididymal cysts, multiple pancreatic cysts, and multiple, bilateral renal tumours and cysts. The patient had no family history of VHL and was negative for germline VHL mutation by standard genetic testing. Further genetic analysis demonstrated a germline balanced translocation between chromosomes 1 and 3, t(1;3)(p36.3;p25) with a breakpoint on chromosome 3 within the second intron of the VHL gene. This created a pathogenic germline alteration in VHL by a novel mechanism that was not detectable by standard genetic testing.Karyotype analysis is not commonly performed in existing genetic screening protocols for patients with VHL. Based on this case, protocols should be updated to include karyotype analysis in patients who are clinically diagnosed with VHL but demonstrate no detectable mutation by existing genetic testing.
    Keywords:  chromosome aberrations; cytogenetic analysis; genetic testing; human genetics; urology
    DOI:  https://doi.org/10.1136/jmedgenet-2020-107308
  9. J Med Genet. 2020 Oct 13. pii: jmedgenet-2020-107059. [Epub ahead of print]
    Blood functional assay for rapid clinical interpretation of germline TP53 variants.
    Sabine Raad, Marion Rolain, Sophie Coutant, Céline Derambure, Raphael Lanos, Françoise Charbonnier, Jacqueline Bou, Emilie Bouvignies, Gwendoline Lienard, Stéphanie Vasseur, Michael Farrell, Olivier Ingster, Stéphanie Baert Desurmont, Edwige Kasper, Gaëlle Bougeard, Thierry Frébourg, Isabelle Tournier.
       BACKGROUND: The interpretation of germline TP53 variants is critical to ensure appropriate medical management of patients with cancer and follow-up of variant carriers. This interpretation remains complex and is becoming a growing challenge considering the exponential increase in TP53 tests. We developed a functional assay directly performed on patients' blood.
    METHODS: Peripheral blood mononuclear cells were cultured, activated, exposed to doxorubicin and the p53-mediated transcriptional response was quantified using reverse transcription-multiplex ligation probe amplification and RT-QMPSF assays, including 10 p53 targets selected from transcriptome analysis, and two amplicons to measure p53 mRNA levels. We applied this blood functional assay to 77 patients addressed for TP53 analysis.
    RESULTS: In 51 wild-type TP53 individuals, the mean p53 functionality score was 12.7 (range 7.5-22.8). Among eight individuals harbouring likely pathogenic or pathogenic variants, the scores were reduced (mean 4.8, range 3.1-7.1), and p53 mRNA levels were reduced in patients harbouring truncating variants. We tested 14 rare unclassified variants (p.(Pro72His), p.(Gly105Asp), p.(Arg110His), p.(Phe134Leu), p.(Arg158Cys), p.(Pro191Arg), p.(Pro278Arg), p.(Arg283Cys), p.(Leu348Ser), p.(Asp352Tyr), p.(Gly108_Phe109delinsVal), p.(Asn131del), p.(Leu265del), c.-117G>T) and 12 yielded functionally abnormal scores. Remarkably, the assay revealed that the c.*1175A>C polymorphic variant within TP53 poly-adenylation site can impact p53 function with the same magnitude as a null variant, when present on both alleles, and may act as a modifying factor in pathogenic variant carriers.
    CONCLUSION: This blood p53 assay should therefore be a useful tool for the rapid clinical classification of germline TP53 variants and detection of non-coding functional variants.
    Keywords:  clinical laboratory techniques; genetic predisposition to disease; genetic testing; germ-line mutation; methods
    DOI:  https://doi.org/10.1136/jmedgenet-2020-107059
  10. Cancers (Basel). 2020 Oct 13. pii: E2962. [Epub ahead of print]12(10):
    GATA2 Related Conditions and Predisposition to Pediatric Myelodysplastic Syndromes.
    Antonella Bruzzese, Davide Leardini, Riccardo Masetti, Luisa Strocchio, Katia Girardi, Mattia Algeri, Giada Del Baldo, Franco Locatelli, Angela Mastronuzzi.
      Myelodysplastic syndromes (MDS) are hematopoietic disorders rare in childhood, often occurring in patients with inherited bone marrow failure syndromes or germinal predisposition syndromes. Among the latter, one of the most frequent involves the gene GATA binding protein 2 (GATA2), coding for a transcriptional regulator of hematopoiesis. The genetic lesion as well as the clinical phenotype are extremely variable; many patients present hematological malignancies, especially MDS with the possibility to evolve into acute myeloid leukemia. Variable immune dysfunction, especially resulting in B- and NK-cell lymphopenia, lead to severe infections, including generalized warts and mycobacterial infection. Defects of alveolar macrophages lead to pulmonary alveolar proteinosis through inadequate clearance of surfactant proteins. Currently, there are no clear guidelines for the monitoring and treatment of patients with GATA2 mutations. In patients with MDS, the only curative treatment is allogeneic hematopoietic stem cell transplantation (HSCT) that restores normal hematopoiesis preventing the progression to acute myeloid leukemia and clears long-standing infections. However, to date, the donor type, conditioning regimen, and the optimal time to proceed to HSCT, as well as the level of chimerism needed to reverse the phenotype, remain unclear highlighting the need for consensus guidelines.
    Keywords:  GATA2 deficiency; cancer predisposition; childhood MDS; myelodysplastic syndromes; pediatric cancer
    DOI:  https://doi.org/10.3390/cancers12102962
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