Open Access

Absence of subtelomeric rearrangements in selected patients with mental retardation as assessed by multiprobe T FISH

  • Suely Rodrigues dos Santos1Email author and
  • Dértia Villalba Freire-Maia2
Journal of Negative Results in BioMedicine201211:16

DOI: 10.1186/1477-5751-11-16

Received: 12 May 2012

Accepted: 18 December 2012

Published: 21 December 2012

Abstract

Background

Mental retardation (MR) is a heterogeneous condition that affects 2-3% of the general population and is a public health problem in developing countries. Chromosomal abnormalities are an important cause of MR and subtelomeric rearrangements (STR) have been reported in 4-35% of individuals with idiopathic MR or an unexplained developmental delay, depending on the screening tests and patient selection criteria used. Clinical checklists such as that suggested by de Vries et al. have been used to improve the predictive value of subtelomeric screening.

Findings

Fifteen patients (1–20 years old; five females and ten males) with moderate to severe MR from a genetics outpatient clinic of the Gaffrée and Guinle Teaching Hospital (HUGG) of the Federal University of Rio de Janeiro State (UNIRIO) were screened with Multiprobe T FISH after normal high resolution karyotyping. No subtelomeric rearrangements were detected even though the clinical score of the patients ranged from four to seven.

Conclusion

In developing countries, FISH-based techniques such as Multiprobe T FISH are still expensive. Although Multiprobe T FISH is a good tool for detecting STR, in this study it did not detect STR in patients with unexplained MR/developmental delay even though these patients had a marked chromosomal imbalance. Our findings also show that clinical scores are not reliable predictors of STR.

Keywords

Developmental delay Mental retardation Subtelomeric rearrangements

Background

Chromosomal abnormalities are an important cause of mental retardation (MR) [1]. Most of these abnormalities can be detected by G-banding karyotype analysis, although subtle structural variations are not easily assessed. Most deletions are located near telomeric regions, a common feature in MR patients [2]. Unfortunately, in most patients (60%) the etiology of MR remains unclear [3], despite the use of good quality metaphase preparations in high resolution assays [4].

In subtelomeric regions, the distal segment is shared by many chromosomes while the proximal is larger and shared by a smaller subset of chromosomes [5]. Sequence similarity between non-homologous chromosomes may cause ectopic recombination during meiosis and lead to subtelomeric rearrangements (STRs) [6], with most translocations occurring in these regions [5]. The frequency of STRs in individuals with MR is 4-35% [7], depending on the assays and patient selection criteria used.

Multiprobe T FISH (MT-FISH) [8] is a specific method for detecting STRs in patients with MR who have a normal karyotype; this technique is widely used in this field of investigation and is available commercially. The wide range in the frequency of STR reflects variation in individual responses in this assay, as well as the availability of adequate laboratory infrastructure [9]. These factors must be considered when choosing the appropriate method in studies of STRs.

The primary aim of this study was to assess the usefulness of MT-FISH as a routine diagnostic test for detecting STRs in children and adolescents with early developmental delay, before the onset of MR. A secondary aim was to improve the predictive value of subtelomeric screening in patients selected using the protocol of de Vries et al. [10]. These individuals had evidence strongly suggestive of a chromosomal imbalance, despite a family history of MR.

Materials and methods

Patient selection

Patients were recruited from the genetics outpatient clinic of HUGG-UNIRIO. The cohort consisted of 15 patients (five females and ten males; age range: 1–20 years old) with learning disabilities and/or MR who presented developmental delay. These subjects had a variable family history of learning disabilities, developmental delay or MR and a normal karyotype, as assessed with a high resolution assay. Dysmorphic features, congenital defects or malformations were recorded systematically during clinical examination. An unknown cause of learning disabilities, developmental delay or MR, or uncommon features in known syndromes, were considered as inclusion criteria. Two sets of twins with the same clinical presentation and two second-grade male cousins without similar clinical features were included in the sample. Tests for fragile X syndrome were done in all males and, to exclude other possible causes of MR, the patients were screened for inborn errors of metabolism and underwent serology tests for toxoplasmosis, rubella, cytomegalovirus, herpes virus and syphilis [11]. Subsequently, the clinical criteria of de Vries et al. [10] were applied and a score of 3 was chosen as the minimum for selecting patients for MT-FISH. All parents/guardians of the patients signed an informed consent form prior to participation in the study. Ethical approval was obtained from the appropriate hospital committees. (HUGG – CEP:22/2003; HSP/UNIFESP CEP: 1070/08).

Cytogenetic technique and molecular cytogenetic analysis

Cytogenetic analysis

Cytogenetic analyses done in the Cytogenetic Laboratory at UNIRIO were used to exclude known chromosomal abnormalities. Lymphocyte cultures were established and harvested using standard protocols for high resolution assays. The quality of the metaphase preparations for karyotype analysis and FISH was enhanced by using Cytoclear® (Genial Genetics Upton, Wirral, UK), according to the manufacturer’s protocol.

Molecular cytogenetics

STRs were detected using Chromoprobe Multiprobe T System® kits (Cytocell Inc., Banbury, UK) with slight modification to the protocol. Hybridization, washing and staining were done according to standard protocols. The test was repeated if more than two probes could not be scored in the multiprobe device. If one or two probes could not be scored then a specific telomeric probe was used to assess the abnormal result. If an alteration was confirmed, FISH was done in the parents to assess whether the abnormality was inherited. Photographic documentation was used only in abnormal cases.

Results

Table 1 shows the clinical and laboratory findings for the 15 patients. Ten patients had a familial history of MR, eight had an abnormal electroencephalogram, seven had central nervous system abnormalities detected by tomography or magnetic resonance, seven had mild malformations or birth defects, five had abnormal vision and one had dysacusis.
Table 1

Clinical data, complementary exams and familial history of patients

Patients ID

MSA

COA

JOS

CCBN

MCSF

AJSF

YPM

JPM

RBB

RoBB

YMB

WMC

JCTFS

LBP

LAS

File number

622076

537048

486383

568752

616423

561932

537160

537162

569901

569575

565119

379028

491362

577557

578487

Birthday

10/8/1985

19/9/1988

10/9/1992

19/7/1984

26/9/2004

28/1/2002

20/4/1995

20/4/1995

2/9/1997

2/9/1997

28/4/1992

24/6/1989

2/9/1995

13/10/1998

21/9/2001

Gender

F

F

F

F

F

M

M

M

M

M

M

M

M

M

M

BW (g)

2360

3100

2850

3350

2580

2625

2750

3000

2230

3050

3340

3630

2010

1235

2155

BL (cm)

45

45

48

50

48

47

-

-

-

-

48

48

43

39

-

BHC (cm)

31

-

-

-

32

33

-

-

-

-

-

-

-

31

-

Age (years)

20

17

13

20

115/12

4

10

10

82/12

82/12

13

15

9

6

4

W (kg)

49.5

43.9

67

67.5

29.8

12.5

41.5

39.2

27.5

28

34.4

63.5

23

17

11.3

H (cm)

142

134

156

150

134.5

97.5

137.5

134.5

125

128

137.5

160

121.5

111

100

HC (cm)

50.5

52

52.5

53

51.5

44.5

54

53

51

51

52

58

51

49.5

48

MF

Y

N

N

Y

N

Y

N

N

Y

Y

N

N

N

Y

Y

DD

Y

Y

Y

Y

Y

Y

Y

Y

Y

Y

Y

Y

Y

Y

Y

Dysmorphism

Y

Y

Y

Y

Y

Y

Y

Y

Y

Y

Y

Y

Y

Y

Y

CS

N

N

N

N

N

N

N

N

N

N

Y

Y

N

N

N

FH

N

N

N

N

Y

Y

Y

Y

Y

Y

Y

Y

Y

Y

Y

LD/MR

Y/Y

Y/Y

Y/Y

Y/Y

Y/Y

Y/Y

Y/Y

Y/Y

Y/Y

Y/Y

Y/Y

Y/Y

Y/Y

Y/Y

Y/Y

X fragile

NEG

-

NEG

NEG

-

NEG

NEG

NEG

NEG

NEG

NEG

NEG

NEG

NEG

NEG

NeuroEv

Y

Y

Y

Y

-

Y

Y

Y

Y

Y

-

Y

Y

Y

Y

CCT / MR

ANL

NL

NL

NL

NL

NL

NL

NL

ANL

ANL

ANL

ANL

ANL

NL

ANL

EEG

ANL

-

NL

-

-

ANL

NL

NL

ANL

ANL

ANL

ANL

ANL

ANL

NL

TORCHS

NEG

NEG

NEG

NEG

NEG

NEG

NEG

NEG

NEG

NEG

NEG

NEG

ANL

NEG

NEG

IEM

NEG

NEG

I

NEG

NEG

NEG

I

I

I

I

NEG

NEG

NEG

NEG

I

BERA

NL

NL

NL

NL

NL

-

NL

NL

-

-

NL

NL

ANL

NL

NL

Ophtalmo Ev

NL

NL

NL

NL

NL

NL

ANL

ANL

NL

NL

NL

ANL

ANL

NL

ANL

DeVries

8

5

4

5

7

8

4

5

5

7

6

5

8

8

7

Birth Weight (BW); Birth Length (BL); Birth Head Circumference (BHC); Weight (W); Height (H); Head Circumference (HC); Malformation (MF); Developmental Delay (DD); Consanguinity; (CS) Familial History (FH); Learning Disabilities (LD)/ Mental Retardation (MR); Neurologic Evaluation (NeuroEv); Cranio Computerized Tomography (CCT) or Cranio Magnetic Resonance (CMR); Electroencephalography (EEG); Toxoplasmosis, rubella, citomegalovirus, herpes virus and syphilis sorology (TORCHS); Inborn Erros of Metabolism (IEM); otoacustic potencials evoked evaluation (BERA); Ophtalmo Evaluation (Ophtalmo Ev).

Female (F); Male (M); Yes (Y); No (N); Negative (NEG); Inconclusive (I); Normal (NL); Abnormal (ANL) clinical score (DeVries).

Normal subtelomeric FISH results were observed in 14 cases. A 13q deletion was suspected in one proband of one set of twins (Figure 1), but a specific telomeric probe did not confirm this (Figure 2). The individual concerned was an eight-year-old boy with severe developmental delay who was a compulsive crier when younger and had mild dysmorphic features. He was the first twin born to a young, healthy, non-consanguineous couple with a family history of MR. His brother had similar clinical features but dissimilar results. FISH analysis of their parents revealed no abnormalities. MT-FISH did not detect STRs in any of the patients.
https://static-content.springer.com/image/art%3A10.1186%2F1477-5751-11-16/MediaObjects/12952_2012_Article_120_Fig1_HTML.jpg
Figure 1

Deletion suspected by MT-FISH.

https://static-content.springer.com/image/art%3A10.1186%2F1477-5751-11-16/MediaObjects/12952_2012_Article_120_Fig2_HTML.jpg
Figure 2

No deletion with 13q subtelomeric probe.

Discussion

MT-FISH is a precise tool for detecting STRs, but its high cost means that in many developing countries it is first necessary to exclude other more common conditions before choosing this technique. For this reason, we have developed a clinical protocol for investigating the causes of MR [12, 13] that can be applied to children suspected of having MR before opting for expensive modern techniques.

Our patients were selected from a large group in which developmental delay was the principal diagnosis and was associated with dysmorphic features and/or malformations. This relationship was initially established in a large screening study in which STRs were found to contribute significantly to unexplained developmental delay and MR with or without a family history of developmental delay or MR [14, 15]. In the last decade, several studies using unselected and selected patients have shown that STRs are a prominent cause of MR, especially in idiopathic forms or unexplained developmental delay. Yu et al. [16] reported that the frequency of truly cryptic subtelomeric abnormalities in selected patients was 2.6%. In this study, we examined whether MT-FISH could be used as a routine diagnostic test before the onset of MR. However, this question could not be answered because no STRs were detected in our patients.

Scoring based on clinical criteria has been used in many studies [1722] to increase the sensitivity of STR detection when MT-FISH is used. De Vries et al. [10] re-examined 29 patients with STRs with regard to their shared characteristics and compared the findings with an MR group without STRs (110 patients). Our group of subjects contained five patients with a low birth weight and nine with a family history of MR. A genetic cause is presumed to underlie half of the cases of undiagnosed patients with idiopathic forms of MR and in many cases there is a family history of MR [12]. Riegel et al. [14] stated that family history was an important selection criterion, especially when MR was associated with dysmorphic features and/or major malformations and growth retardation. As shown here, the number of patients with a low body weight, malformation and a family history was proportionally similar to that reported by de Vries et al. [10]. While the presence of these characteristics and the moderate to severe degree of MR should have increased the likelihood of identifying an STR [10], no STRs were in fact detected. The clinical scores of our patients ranged from four to seven yet no STRs were detected, even though the patients had been carefully selected and were suspected of having a chromosomal anomaly. A similar conclusion was reached by van Karnebeek et al. [23].

Joyce et al. [6] reported one case of STR using MT-FISH that, after a detailed karyotypic review, was found to have semi-cryptic structural anomalies involving a chromosomal imbalance. In the same study, two STRs were found in normal individuals, which suggested polymorphism in subtelomeric regions [24].

A 13q deletion with mosaicism was detected in one of our patients; however, there was no phenotypic correlation with the clinical manifestations [25] and FISH with a specific subtelomeric probe was negative. This case indicates the need to establish a clinical correlation with the cytogenetic findings when an STR is detected, especially if the parents or a specific probe are unavailable.

A non-subtelomeric rearrangement could also explain our negative MT-FISH results. In this case, other techniques such as array comparative genomic hybridization may be useful. Based on our findings, we cannot exclude unknown monogenic disease or multi-factorial conditions as at least part of the etiology of MR and developmental delay in these patients.

Conclusion

In developing countries, there is a need for guidelines for investigating idiopathic MR or unexplained developmental delay in order to establish the best method for a given investigation prior to screening with advanced techniques. MT-FISH is a good tool for investigating the etiology of MR or unexplained developmental delay. However, the cost of this technique in developing countries and the low frequency of STRs mean that the use of MT-FISH may not always be necessary. Finally, clinical criteria were not useful in predicting STRs in this study.

Declarations

Acknowledgements

The authors thank Mariluce Riegel for doing the experiments with the specific telomeric probe, Márcia Pimentel for the molecular evaluation of fragile X chromosome and Maria Lúcia C. Oliveira (LABEIM) for assessing the inborn errors of metabolism. Ivonne Banhos provided partial financial support for this work.

Authors’ Affiliations

(1)
Department of Genetics and Molecular Biology, Federal University of Rio de Janeiro State (DGBM-UNIRIO)
(2)
Department of Morphology and Genetics, Paulista School of Medicine, Federal University of São Paulo (EPM-UNIFESP)

References

  1. Battaglia A, Bianchini E, Carey JC: Diagnostic yield of the comprehensive assessment of developmental delay/mental retardation in an institute of child neuropsychiatry. Am J Med Genet. 1999, 82: 60-66. 10.1002/(SICI)1096-8628(19990101)82:1<60::AID-AJMG12>3.0.CO;2-4.View ArticlePubMed
  2. De Vries BBA, Winter R, Schinzel A, Van Ravenswaaij-Arts C: Telomeres: a diagnosis at the end of the chromosomes. J Med Genet. 2003, 40: 385-98. 10.1136/jmg.40.6.385.PubMed CentralView ArticlePubMed
  3. Auber B, Bruemmer V, Zoll B, Burfeind P, Boehm D, Liehr T, Brockmann K, Wilichowski E, Argyriou L, Bartels I: Identification of subtelomeric genomic imbalances and breakpoint mapping with quantitative PCR in 296 individuals with congenital defects and/or mental retardation. Mol Cytogenet. 2009, 2: 1-11. 10.1186/1755-8166-2-1.View Article
  4. Joyce CA, Dennis NR, Cooper S, Browne CE: Subtelomeric rearrangements: results from a study of selected and unselected probands with idiopathic mental retardation and control individuals by using high-resolution G-banding and FISH. Hum Genet. 2001, 109: 440-51. 10.1007/s004390100588.View ArticlePubMed
  5. Knight S, Flint J: Perfect endings: a review of subtelomeric probes and their use in clinical diagnosis. J Med Genet. 2000, 37: 401-9. 10.1136/jmg.37.6.401.PubMed CentralView ArticlePubMed
  6. Mewborn SK, Martin CL, Ledbetter DH: The dynamic nature and evolutionary history of subtelomeric and pericentromeric regions. Cytogenet Genome Res. 2005, 108: 22-5. 10.1159/000080798.View ArticlePubMed
  7. Velagaleti GVN, Robinson SS, Rouse BM, Tonk VS, Lockhart LH: Subtelomeric rearrangements in idiopathic mental retardation. Indian J Pediatr. 2005, 72: 679-85. 10.1007/BF02724077.View ArticlePubMed
  8. Knight S, Regan R, Nicod A, Horsley SW, Kearney L, Homfray T, Winter RM, Bolton P, Flint J: Subtle chromosomal rearrangements in children with unexplained mental retardation. Lancet. 1999, 354: 1676-81. 10.1016/S0140-6736(99)03070-6.View ArticlePubMed
  9. Erjavec-Skerget A, Stangler-Herodez S, Zagorac A, Zagradisnik B, Koklj-Vokac N: Subtelomeric chromosome rearrangements in children with idiopathic mental retardation: applicability of three molecular-cytogenetic methods. Croat Med J. 2006, 47: 841-50.PubMed CentralPubMed
  10. DeVries BBA, White SM, Knight SJL, Regan R, Homfray T, Young ID, Super M, McKeown C, Splitt M, Quarrell OW, Trainer AH, Niermeijer MF, Malcolm S, Flint J, Hurst JA, Winter RM: Clinical studies on submicroscopic subtelomeric rearragements: a checklist. J Med Genet. 2001, 38: 145-50. 10.1136/jmg.38.3.145.View Article
  11. Curry C, Stevenson RE, Aughton D, Byrne J, Carey JC, Cassidy S, Cunniff C, Graham Jr JM, Jones MC, Kaback MM, Moeschler J, Schaefer B, Schwartz S, Tarleton J, Opitz J: Evaluation of mental retardation: recommendations of a consensus conference. Am J Med Genet. 1997, 72: 468-77. 10.1002/(SICI)1096-8628(19971112)72:4<468::AID-AJMG18>3.0.CO;2-P.View ArticlePubMed
  12. Moeschler JB, Shevell M, and the Commitee on Genetics: Clinical genetic evaluation of the child with mental retardation or devepmental delays. Pediatrics. 2006, 117 (6): 2304-2316. 10.1542/peds.2006-1006.View ArticlePubMed
  13. Council on Children with Disabilities: Identifying infants and young children with development delay disorders in the medical home: an algorithm for developmental surveillance and screening. Pediatrics. 2006, 118: 405-412.View Article
  14. Riegel M, Baumer A, Jamar M, Delbecque K, Herens C, Verloes A, Schinzel A: Submicroscopic terminal deletions and duplications in retarded patients with unclassified malformations syndromes. Hum Genet. 2001, 109: 286-94. 10.1007/s004390100585.View ArticlePubMed
  15. Baker E, Hinton L, Callen DF, Altree M, Dobbie A, Eyre HJ, Sutherland GR, Thompson E, Thompson P, Woollat E, Haan E: Study of 250 children with idiopathic mental retardation reveals nine cryptic and diverse subtelomeric chromosome anomalies. Am J Med Genet. 2002, 107: 285-93. 10.1002/ajmg.10159.View ArticlePubMed
  16. Yu S, Baker E, Hinton L, Eyre HJ, Waters W, Higgins S, Sutherland GR, Haan E: Frequency of truly cryptic subtelomere abnormalities - a study of 534 patients and literature review. Clin Genet. 2005, 68: 436-41. 10.1111/j.1399-0004.2005.00513.x.View ArticlePubMed
  17. Clarkson B, Pavenski K, Dupuis L, Kennedy S, Meyn S, Nezarati MM, Nie G, Weksberg R, Withers S, Quercia N, Teebi AS, Teshima I: Detecting rearrangements in children using subtelomeric FISH and SKY. Am J Med Genet. 2002, 107: 267-74. 10.1002/ajmg.10240.View ArticlePubMed
  18. Dawson AJ, Putnam S, Schultz J, Riordan D, Prasad C, Greenberg CR, Chodirker BN, Mhanni AA, Chudley AE: Cryptical chromosome rearrangements detected by subtelomere assay in patients with mental retardation and dysmorphic features. Clin Genet. 2002, 62: 488-94.View ArticlePubMed
  19. Novelli A, Ceccarini C, Bernardini L, Zuccarello D, Caputo V, Digilio MC, Mingarelli R, Dallapiccola B: High frequency of subtelomeric rearrangements in a cohort of 92 patients with severe mental retardation and dysmorphism. Clin Genet. 2004, 66: 30-38. 10.1111/j.0009-9163.2004.00270.x.View ArticlePubMed
  20. Baroncini A, Rivieri F, Capucci A, Croci G, Franchi F, Sensi A, Battaglia P, Aiello V, Calzolari E: FISH screening for subtelomeric rearrangements in 219 patients with idiopathic mental retardation and normal karyotype. Eur J Med Genet. 2005, 48: 388-96. 10.1016/j.ejmg.2005.05.002.View ArticlePubMed
  21. Rooms L, Reyniers E, van Luijk R, Scheers S, Wauters J, Kooy RF: Subtelomeric rearrangemnts in the mentally retarded: a comparison of detection methods. Hum Mutat. 2005, 25: 513-524. 10.1002/humu.20185.View ArticlePubMed
  22. Palomares M, Delicado A, Lapunzina P, Arjona D, Amiñoso C, Arcas J, Bermejo AM, Fernández L, López Pajares I: MLPA vs Multiprobe T FISH: comparision of two methods for the screening of subtelomeric rearrangements in 50 patients with idiopathic mental retardation. Clin Genet. 2006, 69: 228-233. 10.1111/j.1399-0004.2006.00567.x.View ArticlePubMed
  23. van Karnebeek CDM, Koevoets C, Sluijter S, Bijlsma EK, Smeets DFMC, Redeker EJ, Hennekam RCM, Hoovers JMN: Prospective screening for subtelomeric rearrangements in children with mental retardation of unknown aetiology: the Amsterdam experience. J Med Genet. 2002, 39: 546-53. 10.1136/jmg.39.8.546.PubMed CentralView ArticlePubMed
  24. Ballif B, Kashork CD, Shaffer LG: The promise and pitfalls of telomere region-specific probes. Am J Hum Genet. 2000, 67: 1356-59.PubMed CentralView ArticlePubMed
  25. Pfiffer RA, Ott R, Gilgenkrantz S, Alexandre P: Deficiency of coagulation factor VII and X associated with deletion of a chromosome 13(q34). Evidence from two cases with 46, XY, t(13;Y)(q34;q11). Hum Genet. 1982, 62: 358-60. 10.1007/BF00304557.View Article

Copyright

© Santos and Freire-Maia; licensee BioMed Central Ltd. 2012

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.