Clinical utility of multiplex ligation-dependent probe amplification technique in identification of aetiology of unexplained mental retardation: a study in 203 Indian patients

Abstract

Background & objectives: Developmental delay (DD)/mental retardation also described as intellectual disability (ID), is seen in 1-3 per cent of general population. Diagnosis continues to be a challenge at clinical level. With the advancement of new molecular cytogenetic techniques such as cytogenetic microarray (CMA), multiplex ligation-dependent probe amplification (MLPA) techniques, many microdeletion/microduplication syndromes with DD/ID are now delineated. MLPA technique can probe 40-50 genomic regions in a single reaction and is being used for evaluation of cases with DD/ID. In this study we evaluated the clinical utility of MLPA techniques with different probe sets to identify the aetiology of unexplained mental retardation in patients with ID/DD.

Methods: A total of 203 randomly selected DD/ID cases with/without malformations were studied. MLPA probe sets for subtelomeric regions (P070/P036) and common microdeletions/microduplications (P245-A2) and X-chromosome (P106) were used. Positive cases with MLPA technique were confirmed using either fluorescence in situ hybridization (FISH) or follow up confirmatory MLPA probe sets.

Results: The overall detection rate was found to be 9.3 per cent (19 out of 203). The detection rates were 6.9 and 7.4 per cent for common microdeletion/microduplication and subtelomeric probe sets, respectively. No abnormality was detected with probe set for X-linked ID. The subtelomeric abnormalities detected included deletions of 1p36.33, 4p, 5p, 9p, 9q, 13q telomeric regions and duplication of 9pter. The deletions/duplications detected in non telomeric regions include regions for Prader Willi/Angelman regions, Williams syndrome, Smith Magenis syndrome and Velocardiofacial syndrome.

Interpretation & conclusions: Our results show that the use of P245-A2 and P070/P036-E1 probes gives good diagnostic yield. Though MLPA cannot probe the whole genome like cytogenetic microarray, due to its ease and relative low cost it is an important technique for evaluation of cases with DD/ID.

Fig. 1

(a) & (b) Facial features of representative case no.2137 with 9q34.3 deletion, note flat face and prognathism. (c & d) MLPA P070 and P036-E1 probe sets results of case no. 2137 showing deletion of 9q34. (e) Facial features of case No.2877 with 4p16.33 deletion, note hypertelorism. (f) MLPA results of case 2877 using P373 confirmatory probe set showing deletion of 4p16.33. (g) FISH result of case 2275 showing single copy of 7q11.2 (pink signal). Green signals are controls (2 copies) (h) MLPA profile showing deletion at 7q11.29 using P245-A2 probe set (i) MLPA profile showing deletion at 7q11.29 using P374 confirmatory probe set.

Fig. 2

(a) Case no. 2222- Deletion 1pter. Note straight eybrows (b) Case no. 2364 - Deletion 1pter. Note deep seated eyes (c) Case no. 2604 –Deletion 9pter (d) Case no. 2582- Deletion of 13qter (e) Case no. 2268- Deletion 15q11.2 with features though not characteristic but supportive of Angelman syndrome.