Constitutional Mismatch Repair-deficiency and Whole-exome Sequencing as the Means of the Rapid Detection of the Causative MSH6 Defect

Abstract

Background: Cases of children with more than one type of cancer either diagnosed simultaneously or successively, rarely occur in pediatric oncology. A second malignant neoplasm may be caused by mutagenic effects of the treatment of the primary malignancy and/or may point towards an underlying genetic cancer susceptibility syndrome. One example of such a syndrome is constitutional mismatch repair-deficiency, (CMMR-D) which carries an increased risk of various tumors including childhood hematologic malignancies and Lynch syndrome associated tumors. Timely diagnosis of CMMR-D is crucial, since this diagnosis has implications for the entire family.

Patient: We report the case of a 15-year-old girl who was born to consanguineous parents. At the age of 20 months she was diagnosed with a T-cell non-Hodgkin lymphoma. Treatment was given according to NHL-BFM 95. 12 years later, an invasive adenocarcinoma of the colon was surgically removed which relapsed shortly afterwards.

Methods: Whole-exome sequencing of germline DNA was employed to rapidly detect the underlying mutation in this suspected CMMR-D patient.

Results: After a short turnaround time of less than 3 weeks, the diagnosis of CMMR-D could be confirmed by the identification of a homozygous 29-bp deletion in MSH6 (exon 6), which was confirmed by independent methods.

Conclusions: We demonstrate that “bed-side” whole-exome sequencing is both feasible and cost-effective and may be the method of choice to rapidly uncover the genetical basis of (inherited) diseases.

Zusammenfassung

Hintergrund: Kinder mit 2 verschiedenen Malignomen, die entweder zeitgleich oder sukzessiv diagnostiziert werden, sind in der pädiatrischen Onkologie eine Rarität. Eine zweite Krebserkrankung kann entweder durch die Primärtherapie des Ersttumors verursacht worden sein oder kann auf ein zu Grunde liegendes erbliches Krebssyndrom hinweisen. Ein Beispiel hierfür ist die sogenannte constitutional mismatch repair-deficiency (CMMR-D), welche charakterisiert ist durch ein erhöhtes Tumorrisiko von u. a. malignen hämatolischen Erkrankungen und Lynch-Syndrom-assoziierten Tumoren. Eine zeitnahe Diagnosestellung ist hierbei entscheidend, da diese Diagnose Auswirkungen für die gesamte Familie mit sich bringt.

Patient: Vorgestellt wird der Fall eines 15 Jahre alten Mädchens konsanguiner Eltern. Im Alter von 20 Monaten wurde ein mediastinales T-Zell Non-Hodgkin-Lymphom diagnostiziert. 12 Jahre später wurde ein invasiv wachsendes Adenokarzinom des Kolons chirurgisch entfernt, welches kurze Zeit später rezidivierte.

Methoden: Um die zu Grunde liegende Mutation dieses putativen erblichen Krebssyndroms möglichst rasch zu identifizieren wurde eine Gesamt-Exom-Sequenzierung durchgeführt.

Resultate: Nur 3 Wochen nach Blutentnahme konnten wir die Diagnose CMMR-D durch den Nachweis einer homozygoten, 29 Basenpaare umfassenden Deletion im MSH6 Gen (Exon 6) stellen. Die Deletion konnte in unabhängigen Experimenten validiert werden.

Schlussfolgerungen: Patientennahe Gesamt-Exom-Sequenzierung ist sowohl praktikabel als auch kosteneffektiv. Sie ist die Methode der Wahl zur Charakterisierung des zu Grunde liegenden genetischen Defekts bei (Erb-) Krankheiten.

Key words

childhood cancer syndrome - constitutional mismatch repair syndrome - whole-exome sequencing - genetic testing

Schlüsselwörter

erbliche Krebssyndrome - constitutional mismatch repair syndrome - Gesamt-Exom-Sequenzierung - genetische Testung

• References

• 1 Adzhubei IA, Schmidt S, Peshkin L et al. A method and server for predicting damaging missense mutations. Nat Methods 2010; 7: 248-249
• 2 Ambrose M, Gatti RA. Pathogenesis of ataxia-telangiectasia: the next generation of ATM functions. Blood 2013; 121: 4036-4045
• 3 Baas AF, Gabbett M, Rimac M et al. Agenesis of the corpus callosum and gray matter heterotopia in three patients with constitutional mismatch repair deficiency syndrome. Eur J Hum Genet 2013; 21: 55-61
• 4 Bakry D, Aronson M, Durno C et al. Genetic and clinical determinants of constitutional mismatch repair deficiency syndrome: report from the constitutional mismatch repair deficiency consortium. Eur J Cancer 2014; 50: 987-996
• 5 Bruwer Z, Algar U, Vorster A et al. Predictive Genetic Testing in Children: Constitutional Mismatch Repair Deficiency Cancer Predisposing Syndrome. J Genet Couns 2013;
• 6 Chen C, Bartenhagen C, Gombert M et al. Next-generation-sequencing-based risk stratification and identification of new genes involved in structural and sequence variations in near haploid lymphoblastic leukemia. Genes Chromosomes Cancer 2013; 52: 564-579
• 7 Chou J, Ohsumi TK, Geha RS. Use of whole exome and genome sequencing in the identification of genetic causes of primary immunodeficiencies. Curr Opin Allergy Clin Immunol 2012; 12: 623-628
• 8 DePristo MA, Banks E, Poplin R et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 2011; 43: 491-498
• 9 Duraku LS, Hossaini M, Schuttenhelm BN et al. Re-innervation patterns by peptidergic Substance-P, non-peptidergic P2 X 3, and myelinated NF-200 nerve fibers in epidermis and dermis of rats with neuropathic pain. Exp Neurol 2013; 241: 13-24
• 10 Fisher S, Barry A, Abreu J et al. A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Genome Biol 2011; 12: R1
• 11 Jones MA, Ng BG, Bhide S et al. DDOST mutations identified by whole-exome sequencing are implicated in congenital disorders of glycosylation. Am J Hum Genet 2012; 90: 363-368
• 12 Kargl S, Meissl M, Pumberger W. Early Postnatal Diagnosis of Costello Syndrome. Klin Padiatr 2010;
• 13 Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 2009; 4: 1073-1081
• 14 Leach FS, Nicolaides NC, Papadopoulos N et al. Mutations of a mutS homolog in hereditary nonpolyposis colorectal cancer. Cell 1993; 75: 1215-1225
• 15 Leenen CH, Geurts-Giele WR, Dubbink HJ et al. Pitfalls in molecular analysis for mismatch repair deficiency in a family with biallelic pms2 germline mutations. Clin Genet 2011; 80: 558-565
• 16 Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010; 26: 589-595
• 17 Li H, Handsaker B, Wysoker A et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009; 25: 2078-2079
• 18 Livingstone E, Caliebe A, Egberts F et al. Malignant melanoma and Wiedemann-Beckwith syndrome in childhood. Klin Padiatr 2010; 222: 388-390
• 19 McDonell LM, Mirzaa GM, Alcantara D et al. Mutations in STAMBP, encoding a deubiquitinating enzyme, cause microcephaly-capillary malformation syndrome. Nat Genet 2013; 45: 556-562
• 20 McLaren W, Pritchard B, Rios D et al. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 2010; 26: 2069-2070
• 21 Ripperger T, Beger C, Rahner N et al. Constitutional mismatch repair deficiency and childhood leukemia/lymphoma – report on a novel biallelic MSH6 mutation. Haematologica 2010; 95: 841-844
• 22 Rosenbaum T, Wimmer K. Neurofibromatosis type 1 (NF1) and Associated Tumors. Klin Padiatr 2013;
• 23 Schultze-Florey RE, Graf N, Vorwerk P et al. DICER1 syndrome: a new cancer syndrome. Klin Padiatr 2013; 225: 177-178
• 24 Shah SN, Hile SE, Eckert KA. Defective mismatch repair, microsatellite mutation bias, and variability in clinical cancer phenotypes. Cancer Res 2010; 70: 431-435
• 25 Thompson BA, Spurdle AB, Plazzer JP et al. Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database. Nat Genet 2013; 46: 107-115
• 26 Varley JM. Germline TP53 mutations and Li-Fraumeni syndrome. Hum Mutat 2003; 21: 313-320
• 27 Vasen HF, Ghorbanoghli Z, Bourdeaut F et al. Guidelines for surveillance of individuals with constitutional mismatch repair-deficiency proposed by the European Consortium “Care for CMMR-D” (C4CMMR-D). J Med Genet 2014; 51: 283-293
• 28 Wessalowski R, Schneider DT, Mils O et al. Regional deep hyperthermia for salvage treatment of children and adolescents with refractory or recurrent non-testicular malignant germ-cell tumours: an open-label, non-randomised, single-institution, phase 2 study. Lancet Oncol 2013; 14: 843-852
• 29 Wimmer K, Etzler J. Constitutional mismatch repair-deficiency syndrome: have we so far seen only the tip of an iceberg?. Hum Genet 2008; 124: 105-122
• 30 Wimmer K, Kratz CP. Constitutional mismatch repair-deficiency syndrome. Haematologica 2010; 95: 699-701
• 31 Wimmer K, Kratz CP, Vasen HF et al. Diagnostic criteria for constitutional mismatch repair deficiency syndrome: suggestions of the European consortium ‘care for CMMRD’ (C4CMMRD). J Med Genet 2014; 51: 355-365
• 32 Wimmer K, Kratz CP, Vasen HF et al. Diagnostic criteria for constitutional mismatch repair deficiency syndrome: suggestions of the European consortium ‘Care for CMMRD’ (C4CMMRD). J Med Genet 2014; Published Online First 2014/04/15
• 33 Yang Y, Muzny DM, Reid JG et al. Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N Engl J Med 2013; 369: 1502-1511