Pathogenic variants affecting the BLM gene are responsible for the manifestation of extremely rare cancer‑predisposing Bloom syndrome. The present study reports on a case of an infant with a congenital hypotrophy, short stature and abnormal facial appearance. Initially she was examined using a routine molecular diagnostic algorithm, including the cytogenetic analysis of her karyotype, microarray analysis and methylation‑specific MLPA, however, she remained undiagnosed on a molecular level. Therefore, she and her parents were enrolled in the project of trio‑based exome sequencing (ES) using Human Core Exome kit. She was revealed as a carrier of an extremely rare combination of causative sequence variants altering the BLM gene (NM_000057.4), c.1642C>T and c.2207_2212delinsTAGATTC in the compound heterozygosity, resulting in a diagnosis of Bloom syndrome. Simultaneously, a mosaic loss of heterozygosity of chromosome 11p was detected and then confirmed as a borderline imprinting center 1 hypermethylation on chromosome 11p15. The diagnosis of Bloom syndrome and mosaic copy‑number neutral loss of heterozygosity of chromosome 11p increases a lifetime risk to develop any types of malignancy. This case demonstrates the trio‑based ES as a complex approach for the molecular diagnostics of rare pediatric diseases.

Biosciences Institute Newcastle University Newcastle upon Tyne NE2 4HH United Kingdom

Department of Experimental Biology Faculty of Science Masaryk University 61137 Brno Czech Republic

Department of Medical Genetics and Genomics University Hospital Brno 62500 Brno Czech Republic

Laboratory of Cytogenomics Centre of Molecular Biology and Genetics Department of Internal Medicine Hematology and Oncology University Hospital Brno 62500 Brno Czech Republic

Zobrazit více v PubMed

Posey JE. Genome sequencing and implications for rare disorders. Orphanet J Rare Dis. 2019;14:153. doi: 10.1186/s13023-019-1127-0. PubMed DOI PMC

Cummings BB, Marshall JL, Tukiainen T, Lek M, Donkervoot S, Foley AR, Bolduc V, Waddell LB, Sandaradura SA, O'Grady GL, et al. Improving genetic diagnosis in Mendelian disease with transcriptome sequencing. Sci Transl Med. 2017;9:eaal5209. doi: 10.1126/scitranslmed.aal5209. PubMed DOI PMC

Patel DS, Misenko SM, Her J, Bunting SF. BLM helicase regulates DNA repair by counteracting RAD51 loading at DNA double-strand break sites. J Cell Biol. 2017;216:3521–3534. doi: 10.1083/jcb.201703144. PubMed DOI PMC

Cunniff C, Bassetti JA, Ellis NA. Bloom's syndrome: Clinical spectrum, molecular pathogenesis, and cancer predisposition. Mol Syndromol. 2017;8:4–23. doi: 10.1159/000452082. PubMed DOI PMC

Traverso G, Bettergowda C, Kraus J, Speicher MR, Kinzler KW, Vogelstein B, Lengauer C. Hyper-recombination and genetic instability in BLM-deficient epithelial cells. Cancer Res. 2003;63:8578–8581. PubMed

Vojta V. Rehabilitation des spastischen infantilen syndroms. Eigene Methodik. Orthop Traumat. 1965;12:557–562. PubMed

Howe B, Umrigar A, Tsien F. Chromosome preparation from cultured cells. J Vis Exp. 2014;28:e50203. PubMed PMC

Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(−Delta Delta-C(T)) method. Methods. 2001;25:402–408. doi: 10.1006/meth.2001.1262. PubMed DOI

Wayhelova M, Vallova V, Broz P, Mikulasova A, Loubalova D, Filkova H, Smetana J, Drabova K, Gaillyova R, Kuglik P. Novel de novo pathogenic variant in the GNAI1 gene as a cause of severe disorders of intellectual development. J Hum Genet. 2022;67:209–214. doi: 10.1038/s10038-021-00988-w. PubMed DOI

Chen S, Zhou Y, Chen Y, Gu J. fastp: An ultra-fast-all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:i884–i890. doi: 10.1093/bioinformatics/bty560. PubMed DOI PMC

Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–1760. doi: 10.1093/bioinformatics/btp324. PubMed DOI PMC

Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L. VarScan: Variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics. 2009;25:2283–2285. doi: 10.1093/bioinformatics/btp373. PubMed DOI PMC

R Core Team (2020), corp-author R Foundation for Statistical Computing; Vienna, Austria: R: A language and environment for statistical computing.

McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GRS, Thormann A, Flicek P, Cunningham F. The ensembl variant effect predictor. Genome Biol. 2016;17:122. doi: 10.1186/s13059-016-0974-4. PubMed DOI PMC

Landrum MJ, Lee JM, Benson B, Brown GR, Chao C, Chitipiralla S, Gu B, Hart J, Hoffman D, Jang W, et al. ClinVar: Improving access to variant interpretations and supporting evidence. Nucleic Acids Res. 2018;46:D1062–D1067. doi: 10.1093/nar/gkx1153. PubMed DOI PMC

Kopanos C, Tsiolkas V, Kouris A, Chapple CE, Aguillera MA, Meyer R, Massouras A. VarSome: The human genomic variant search engine. Bioinformatics. 2019;35:1978–1980. doi: 10.1093/bioinformatics/bty897. PubMed DOI PMC

Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA. Online mendelian inheritance in man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 2005;33:D514–D517. doi: 10.1093/nar/gki033. PubMed DOI PMC

Lappalainen I, Lopez J, Skipper L, Hefferson T, Spalding JD, Garner J, Chen C, Maguire M, Corberr M, Zhou G, et al. DbVar and DGVa: Public archives for genomic structural variation. Nucleic Acids Res. 2013;41:D936–D941. doi: 10.1093/nar/gks1213. PubMed DOI PMC

Kendall KM, Bracher-Smith M, Fitzpatrick H, Lynham A, Rees E, Escott-Price V, Owen MJ, O'Donovan MC, Walters JTR, Kirov G. Cognitive performance and functional outcomes of pathogenic copy number variants: Analysis of the UK Biobank. Br J Psychiatry. 2019;214:297–304. doi: 10.1192/bjp.2018.301. PubMed DOI PMC

Miller DT, Lee K, Abul-Husn NS, Amendola LM, Brothers K, Chung WK, Gollob MH, Gordon AS, Harrison SM, Hershberger RE, et al. ACMG SF v3.1 list for reporting of secondary findings in clinical exome and genome sequencing: A policy statement of the American College of medical genetics and genomics (ACMG) Genet Med. 2022;24:1407–1414. doi: 10.1016/j.gim.2022.04.006. PubMed DOI

Li L, Eng C, Desnick RJ, German J, Ellis NA. Carrier frequency of the Bloom syndrome blmAsh mutation in the Ashkenazi Jewish population. Mol Genet Metab. 1998;64:286–290. doi: 10.1006/mgme.1998.2733. PubMed DOI

Montenegro MM, Quaio CR, Palmeira P, Gasparini Y, Rangel-Santos A, Damasceno J, Novak EM, Gimenez TM, Yamamoto GL, Ronjo RS, et al. Gene expression profile suggesting immunological dysregulation in two Brazilian Bloom's syndrome cases. Mol Genet Genomic Med. 2020;8:e1133. doi: 10.1002/mgg3.1133. PubMed DOI PMC

German J, Sanz MM, Ciocci S, Ye TZ, Ellis NA. Syndrome-causing mutations of the BLM gene in persons in the Bloom's syndrome registry. Hum Mutat. 2007;28:743–753. doi: 10.1002/humu.20501. PubMed DOI

Gönenc, Elcioglu NH, Grijalva CM, Aras S, Großmann N, Praulich I, Altmüller J, Kaulfuß S, Li Y, Nürnberg P, et al. Phenotypic spectrum of BLM- and RMI1-related Bloom syndrome. Clin Genet. 2022;101:559–564. doi: 10.1111/cge.14125. PubMed DOI

Backers L, Parton B, De Bruyne M, Tavernier SJ, Van Den Bogaert K, Lambrecht BN, Haerynck F, Claes KBM. Missing heritability in Bloom syndrome: First report of a deep intronic variant leading to pseudo-exon activation in the BLM gene. Clin Genet. 2021;99:292–297. doi: 10.1111/cge.13859. PubMed DOI

Gönenc, Wolff A, Schmidt J, Zibat A, Müller C, Cyganek L, Argyriou L, Räschle M, Yigit G, Wollnik B. Single-cell transcription profiles in Bloom syndrome patients link BLM deficiency with altered condensin complex expression signatures. Hum Mol Genet. 2022;31:2185–2193. doi: 10.1093/hmg/ddab373. PubMed DOI PMC

Suspitsin EN, Sibgatullina FI, Lyazina LV, Imyanitov EN. First two cases of Bloom syndrome in Russia: Lack of skin manifestation in a BLM c.1642C>T (p.Q548X) homozygote as a likely cause of underdiagnosis. Mol Syndromol. 2017;8:103–106. doi: 10.1159/000454820. PubMed DOI PMC

Trizuljak J, Petruchová T, Blaháková I, Vrzalová Z, Hořínová V, Doubková M, Michalka J, Mayer J, Pospíšilová Š, Doubek M. Diagnosis of Bloom syndrome in a patient with short stature, recurrence of malignant lymphoma, and consanguineous origin. Mol Syndromol. 2020;11:73–82. doi: 10.1159/000507006. PubMed DOI PMC

Wan L, Han J, Liu T, Dong S, Xie F, Chen H, Huang J. Scaffolding protein SPIDR/KIAA0146 connects the Bloom syndrome helicase with homologous recombination repair. Proc Natl Acad Sci USA. 2013;110:10646–10651. doi: 10.1073/pnas.1220921110. PubMed DOI PMC

Sokolenko AP, Iyevleva AG, Preobrazhenskaya EV, Mitiushkina NV, Abysheva SN, Suspitsin EN, Kuligina ES, Gorodnova TV, Pfeifer W, Togo AV, et al. High prevalence and breast cancer predisposing role of the BLM c.1642C>T (Q548X) mutation in Russia. Int J Cancer. 2012;130:2867–2873. doi: 10.1002/ijc.26342. PubMed DOI

Prokofyeva D, Bogdanova N, Dubrowinskaja N, Bermisheva M, Takhirova Z, Antonenkova N, Turmanov N, Datsyuk I, Gantsev S, Christiansen H, et al. Nonsense mutation p.Q548X in BLM, the gene mutated in Bloom's syndrome, is associated with breast cancer in Slavic population. Breast Cancer Res Treat. 2013;137:533–539. doi: 10.1007/s10549-012-2357-1. PubMed DOI

Shahrabani-Gargir L, Shomrat R, Yaron Y, Orr-Urteger A, Groden J, Legum C. High frequency of a common Bloom syndrome Ashkenazi mutation among Jews of polish origin. Genet Test. 1998;2:293–296. doi: 10.1089/gte.1998.2.293. PubMed DOI

Huson SM, Staab T, Pereira M, Ward H, Paredes R, Evans DG, Baumhoer D, O'Sullivan J, Cheesman E, Schindler D, Meyer S. Infantile fibrosarcoma with TPM3-NTRK1 fusion in a boy with Bloom syndrome. Fam Cancer. 2022;21:85–90. doi: 10.1007/s10689-020-00221-1. PubMed DOI PMC

Fiala EM, Ortiz MV, Kennedy JA, Glodzik D, Fleischut MH, Duffy KA, Hathaway ER, Heaton T, Gerstle JT, Steinherz P, et al. 11p15.5 epimutations in children with Wilms tumor and hepatoblastoma detected in peripheral blood. Cancer. 2020;126:3114–3121. doi: 10.1002/cncr.32907. PubMed DOI PMC

Ibrahim A, Kirby G, Hardy C, Dias RP, Tee L, Lim D, Berg J, MacDonald F, Nightingale P, Maher ER. Methylation analysis and diagnostics of Beckwith-Wiedemann syndrome in 1,000 subjects. Clin Epigenetics. 2014;6:11. doi: 10.1186/1868-7083-6-11. PubMed DOI PMC

Van Veghel-Plandsoen MM, Wouters CH, Kromosoeto JNR, den Ridder-Klünnen MC, Halley DJJ, van den Ouweland AMW. Multiplex ligation-depending probe amplification is not suitable for detection of low-grade mosaicism. Eur J Hum Genet. 2011;19:1009–1012. doi: 10.1038/ejhg.2011.60. PubMed DOI PMC

Brioude F, Kalish JM, Mussa A, Foster AC, Bliek J, Ferrero GB, Boonen SE, Cole T, Baker R, Bertoletti M, et al. Expert consensus document: Clinical and molecular diagnosis, screening and management of Beckwith-Wiedemann syndrome: An international consensus statement. Nat Rev Endocrinol. 2018;14:229–249. doi: 10.1038/nrendo.2017.166. PubMed DOI PMC

LaRocque JR, Stark JM, Oh J, Bojilova E, Yusa K, Horie K, Takeda J, Jasin M. Interhomolog recombination and loss of heterozygosity in wild-type and Bloom syndrome helicase (BLM)-deficient mammalian cells. Proc Natl Acad Sci USA. 2011;108:11971–11976. doi: 10.1073/pnas.1104421108. PubMed DOI PMC

Bouman A, van Koningsbruggen S, Karakullukcu MB, Schreuder WH, Lakeman P. Bloom syndrome does not always present with sun-sensitive facial erythema. Eur J Med Genet. 2018;61:94–97. doi: 10.1016/j.ejmg.2017.10.010. PubMed DOI

MacFarland SP, Duffy KA, Bhatti TR, Bagatell R, Balamuth NJ, Brodeur GM, Ganguly A, Mattei PA, Surrey LF, Balis FM, Kalish JM. Diagnosis of beckwith-wiedemann syndrome in children presenting with wilms tumor. Pediatr Blood Cancer. 2018;65:e27296. doi: 10.1002/pbc.27296. PubMed DOI PMC

Alders M, Maas SM, Kadouch DJM, var der Lip K, Bliek J, van der Horst CMAM, Mannens MMAM. Methylation analysis in tongue tissue of BWS patients identifies the (EPI)genetic cause in 3 patients with normal methylation levels in blood. Eur J Med Genet. 2014;57:293–297. doi: 10.1016/j.ejmg.2014.03.011. PubMed DOI

Campbell MB, Campbell WC, Rogers J, Rogers N, Rogers Z, van den Hurk AM, Webb A, Webb T, Zaslaw P. Bloom syndrome: Research and data priorities for the development of precision medicine as identified by some affected families. Cold Spring Harb Mol Case Stud. 2018;4:a002816. doi: 10.1101/mcs.a002816. PubMed DOI PMC

Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. Integrative Genomics Viewer. Nat Biotechnol. 2011;29:24–26. doi: 10.1038/nbt.1754. PubMed DOI PMC

Exome sequencing improves the molecular diagnostics of paediatric unexplained neurodevelopmental disorders