Severity Scoring Cutoff for MLPA and Its Diagnostic Yield in 332 North Indian Children with Developmental Delay

 

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Abstract

Chromosomal aberrations/rearrangements are the most common cause of intellectual disability (ID), developmental delay (DD), and congenital malformations. Traditionally, karyotyping has been the investigation of choice in such cases, with the advantage of being cheap and easily accessible, but with the caveat of the inability to detect copy number variations of sizes less than 5 Mb. Chromosomal microarray can solve this problem, but again the problems of expense and poor availability are major challenges in developing countries. The purpose of this study is to find the utility of multiplex ligation-dependent probe amplification (MLPA) as a middle ground, in a resource-limited setting. We also attempted to establish an optimum cutoff for the de Vries score, to enable physicians to decide between these tests on a case-to-case basis, using only clinical data. A total of 332 children with DD/ID with or without facial dysmorphism and congenital malformations were studied by MLPA probe sets P245. Assessment of clinical variables concerning birth history, facial dysmorphism, congenital malformations, and family history was done. We also scored the de Vries scoring for all the patients to find a suitable cutoff for MLPA screening. In our study, the overall detection rate of MLPA was 13.5% (45/332). The majority of patients were DiGeorge's syndrome with probe deletion in 22q11.21 in 3.3% (11/332) followed by 15q11.2 del in 3.6% (12/332, split between Angelman's and Prader–Willi's syndromes). Also, 3.0% (10/332) of patients were positive for Williams–Beuren's syndrome 7q11.23, 1.8% (6/332) for Wolf–-Hirschhorn's syndrome 4p16.3, 1.2% (4/332) for 1p36 deletion, and 1% for each trichorhinophalangeal syndrome type I 8q23.3 duplication syndrome and cri du chat syndrome. The optimum cutoff of de Vries score for MLPA testing in children with ID and/or dysmorphism came out to be 2.5 (rounded off to 3) with a sensitivity of 82.2% and specificity of 66.7%. This is the largest study from India for the detection of chromosomal aberrations using MLPA common microdeletion kit P245. Our study suggests that de Vries score with a cutoff of 3 or more can be used to offer MLPA as the first tier test for patients with unexplained ID, with or without facial dysmorphism and congenital malformations.

Ethics Approval

Institutional ethical clearance has been taken for this study.

Consent to Participate

Written informed consent was obtained from the participants.

Consent to Publish

The authors affirm that human research participants provided informed consent for the publication of the images in [Fig. 3A to E].

Authors' Contributions

All authors contributed to the study conception and design. P.S. contributed to experimentation, result interpretation, and manuscript drafting and writing. P.K. and R.D. contributed to manuscript writing and clinical data compilation. C.C. contributed in clinical data collection and compilation. A.K., S.S., D.K., and R.D. performed the experiments. A.K. and I.P. involved in patient care and management. All authors read and approved the final manuscript.

^* Both the authors share equal first authorship.

Publication History

Received: 18 February 2022

Accepted: 21 August 2022

Article published online:
10 October 2022

© 2022. Thieme. All rights reserved.

Georg Thieme Verlag KG
Rüdigerstraße 14, 70469 Stuttgart, Germany

• References

• 1 American Psychiatric Associations. . In: Jeste DV, Lieberman JA, Fassler D, Peele R. eds. Diagnostic and Statistical Manual of Mental Disorders. 5th ed. Washington: American Psychiatric Publishing; 2013
  CrossrefGoogle Scholar
• 2 Battaglia A, Doccini V, Bernardini L. et al. Confirmation of chromosomal microarray as a first-tier clinical diagnostic test for individuals with developmental delay, intellectual disability, autism spectrum disorders and dysmorphic features. Eur J Paediatr Neurol 2013; 17 (06) 589-599
  CrossrefPubMedGoogle Scholar
• 3 Belkady B, Elkhattabi L, Elkarhat Z. et al. Chromosomal abnormalities in patients with intellectual disability: a 21-year retrospective study. Hum Hered 2018; 83 (05) 274-282
  CrossrefPubMedGoogle Scholar
• 4 Doyle CT. The cytogenetics of 90 patients with idiopathic mental retardation/malformation syndromes and of 90 normal subjects. Hum Genet 1976; 33 (02) 131-146
  CrossrefPubMedGoogle Scholar
• 5 Coco R, Penchaszadeh VB. Cytogenetic findings in 200 children with mental retardation and multiple congenital anomalies of unknown cause. Am J Med Genet 1982; 12 (02) 155-173
  CrossrefPubMedGoogle Scholar
• 6 Vissers LELM, de Vries BBA, Osoegawa K. et al. Array-based comparative genomic hybridization for the genomewide detection of submicroscopic chromosomal abnormalities. Am J Hum Genet 2003; 73 (06) 1261-1270
  CrossrefPubMedGoogle Scholar
• 7 Rauch A, Hoyer J, Guth S. et al. Diagnostic yield of various genetic approaches in patients with unexplained developmental delay or mental retardation. Am J Med Genet A 2006; 140 (19) 2063-2074
  CrossrefPubMedGoogle Scholar
• 8 Coe BP, Witherspoon K, Rosenfeld JA. et al. Refining analyses of copy number variation identifies specific genes associated with developmental delay. Nat Genet 2014; 46 (10) 1063-1071
  CrossrefPubMedGoogle Scholar
• 9 Shevell M, Ashwal S, Donley D. et al; Quality Standards Subcommittee of the American Academy of Neurology, Practice Committee of the Child Neurology Society. Practice parameter: evaluation of the child with global developmental delay: report of the Quality Standards Subcommittee of the American Academy of Neurology and The Practice Committee of the Child Neurology Society. Neurology 2003; 60 (03) 367-380
  CrossrefPubMedGoogle Scholar
• 10 Sadek AA, Mohamed MA. Yield of karyotyping in children with developmental delay and/or dysmorphic features in Sohag University Hospital, Upper Egypt. Egypt J Med Hum Genet 2018; 19 (03) 253-259
  CrossrefPubMedGoogle Scholar
• 11 Miller DT, Adam MP, Aradhya S. et al. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet 2010; 86 (05) 749-764
  CrossrefPubMedGoogle Scholar
• 12 Hastings RJ, Cavani S, Bricarelli FD, Patsalis PC, Kristoffersson U. ECA PWG Co-ordinators. Cytogenetic Guidelines and Quality Assurance: a common European framework for quality assessment for constitutional and acquired cytogenetic investigations. Eur J Hum Genet 2007; 15 (05) 525-527
  CrossrefPubMedGoogle Scholar
• 13 John N, Rajasekhar M, Girisha KM, Sharma PS, Gopinath PM. Multiplex ligation-dependent probe amplification study of children with idiopathic mental retardation in South India. Indian J Hum Genet 2013; 19 (02) 165-170
  CrossrefPubMedGoogle Scholar
• 14 Shaffer LG, Kashork CD, Saleki R. et al. Targeted genomic microarray analysis for identification of chromosome abnormalities in 1500 consecutive clinical cases. J Pediatr 2006; 149 (01) 98-102
  CrossrefPubMedGoogle Scholar
• 15 Schouten JP, McElgunn CJ, Waaijer R, Zwijnenburg D, Diepvens F, Pals G. Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res 2002; 30 (12) e57-e57
  CrossrefPubMedGoogle Scholar
• 16 MRC Holland. SALSA MLPA Probemix P245 Microdeletion Syndromes-1A [Internet]. MRC Holland. [accessed April 22, 2022]. Available at: https://www.mrcholland.com/product/P245/2572
  PubMedGoogle Scholar
• 17 Lee D, Na S, Park S. et al. Clinical experience with multiplex ligation-dependent probe amplification for microdeletion syndromes in prenatal diagnosis: 7522 pregnant Korean women. Mol Cytogenet 2019; 12 (01) 10
  CrossrefPubMedGoogle Scholar
• 18 Konialis C, Savola S, Karapanou S. et al. Routine application of a novel MLPA-based first-line screening test uncovers clinically relevant copy number aberrations in haematological malignancies undetectable by conventional cytogenetics. Hematology 2014; 19 (04) 217-224
  CrossrefPubMedGoogle Scholar
• 19 Prapasrat C, Onsod P, Korkiatsakul V, Rerkamnuaychoke B, Wattanasirichaigoon D, Chareonsirisuthigul T. The utilization of MS-MLPA as the first-line test for the diagnosis of Prader–Willi syndrome in Thai patients. J Pediatr Genet 2022; 12 (04) 273-279
  Article in Thieme ConnectPubMedGoogle Scholar
• 20 Monteiro RAC, de Freitas ML, Vianna GS. et al. Major contribution of genomic copy number variation in syndromic congenital heart disease: the use of MLPA as the first genetic test. Mol Syndromol 2017; 8 (05) 227-235
  CrossrefPubMedGoogle Scholar
• 21 de Vries BB, White SM, Knight SJ. et al. Clinical studies on submicroscopic subtelomeric rearrangements: a checklist. J Med Genet 2001; 38 (03) 145-150
  CrossrefPubMedGoogle Scholar
• 22 Jehee FS, Takamori JT, Medeiros PF. et al. Using a combination of MLPA kits to detect chromosomal imbalances in patients with multiple congenital anomalies and mental retardation is a valuable choice for developing countries. Eur J Med Genet 2011; 54 (04) e425-e432
  CrossrefPubMedGoogle Scholar
• 23 Feenstra I, Hanemaaijer N, Sikkema-Raddatz B. et al. Balanced into array: genome-wide array analysis in 54 patients with an apparently balanced de novo chromosome rearrangement and a meta-analysis. Eur J Hum Genet 2011; 19 (11) 1152-1160
  CrossrefPubMedGoogle Scholar
• 24 MRC Holland. Coffalyser.Net [Internet]. MRC Holland. 2022 [accessed April 22, 2022]. Available at: https://www.mrcholland.com/technology/software/coffalyser-net
  PubMedGoogle Scholar
• 25 IBM. IBM SPSS Statistics [Internet]. IBM. 2022 [cited April 22, 2022]. Available at: https://www.ibm.com/in-en/products/spss-statistics
  PubMedGoogle Scholar
• 26 Ismail SA, McCullough A, Guo S, Sharkey A, Harma S, Rutter P. Gender-related differences in care-seeking behaviour for newborns: a systematic review of the evidence in South Asia. BMJ Glob Health 2019; 4 (03) e001309
  PubMedGoogle Scholar
• 27 Mandal K, Boggula VR, Borkar M, Agarwal S, Phadke SR. Use of Multiplex Ligation-Dependent Probe Amplification (MLPA) in screening of subtelomeric regions in children with idiopathic mental retardation. Indian J Pediatr 2009; 76 (10) 1027-1031
  CrossrefPubMedGoogle Scholar
• 28 Boggula VR, Shukla A, Danda S. et al. Clinical utility of multiplex ligation-dependent probe amplification technique in identification of aetiology of unexplained mental retardation: a study in 203 Indian patients. Indian J Med Res 2014; 139 (01) 66-75
  PubMedGoogle Scholar
• 29 Mohan S, Venkatesan V, Paul SFD, Koshy T, Perumal V. Genomic imbalance in subjects with idiopathic intellectual disability detected by multiplex ligation-dependent probe amplification. J Genet 2016; 95 (02) 469-474
  CrossrefPubMedGoogle Scholar
• 30 Shoukier M, Klein N, Auber B. et al. Array CGH in patients with developmental delay or intellectual disability: are there phenotypic clues to pathogenic copy number variants?. Clin Genet 2013; 83 (01) 53-65
  CrossrefPubMedGoogle Scholar
• 31 Ledbetter DH, Martin CL. Cryptic telomere imbalance: a 15-year update. Am J Med Genet C Semin Med Genet 2007; 145C (04) 327-334
  CrossrefPubMedGoogle Scholar
• 32 Stankiewicz P, Pursley AN, Cheung SW. Challenges in clinical interpretation of microduplications detected by array CGH analysis. Am J Med Genet A 2010; 152A (05) 1089-1100
  CrossrefPubMedGoogle Scholar
• 33 Zepeda-Mendoza CJ, Cousin MA, Basu S. et al. An intragenic duplication of TRPS1 leading to abnormal transcripts and causing trichorhinophalangeal syndrome type I. Cold Spring Harb Mol Case Stud 2019; 5 (06) a004655
  CrossrefPubMedGoogle Scholar