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      Subtelomeric chromosomal rearrangements in a large cohort of unexplained intellectually disabled individuals in Indonesia: A clinical and molecular study

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          Abstract

          CONTEXT:

          Unbalanced subtelomeric chromosomal rearrangements are often associated with intellectual disability (ID) and malformation syndromes. The prevalence of such rearrangements has been reported to be 5-9% in ID populations.

          AIMS:

          To study the prevalence of subtelomeric rearrangements in the Indonesian ID population.

          MATERIALS AND METHODS:

          We tested 436 subjects with unexplained ID using multiplex ligation dependent probe amplification (MLPA) using the specific designed sets of probes to detect human subtelomeric chromosomal imbalances (SALSA P070 and P036D). If necessary, abnormal findings were confirmed by other MLPA probe kits, fluorescent in situ hybridization or Single Nucleotide Polymorphism array.

          RESULTS:

          A subtelomeric aberration was identified in 3.7% of patients (16/436). Details on subtelomeric aberrations and confirmation analyses are discussed.

          CONCLUSION:

          This is the first study describing the presence of subtelomeric rearrangements in individuals with ID in Indonesia. Furthermore, it shows that also in Indonesia such abnormalities are a prime cause of ID and that in developing countries with limited diagnostic services such as Indonesia, it is important and feasible to uncover the genetic etiology in a significant number of cases with ID.

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          Most cited references31

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          A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays.

          Yasuhito Nannya, Masashi Sanada, Kumi Nakazaki … (2005)
          We have developed a robust algorithm for copy number analysis of the human genome using high-density oligonucleotide microarrays containing 116,204 single-nucleotide polymorphisms. The advantages of this algorithm include the improvement of signal-to-noise (S/N) ratios and the use of an optimized reference. The raw S/N ratios were improved by accounting for the length and GC content of the PCR products using quadratic regressions. The use of constitutional DNA, when available, gives the lowest SD values (0.16 +/- 0.03) and also enables allele-based copy number detection in cancer genomes, which can unmask otherwise concealed allelic imbalances. In the absence of constitutional DNA, optimized selection of multiple normal references with the highest S/N ratios, in combination with the data regressions, dramatically improves SD values from 0.67 +/- 0.12 to 0.18 +/- 0.03. These improvements allow for highly reliable comparison of data across different experimental conditions, detection of allele-based copy number changes, and more accurate estimations of the range and magnitude of copy number aberrations. This algorithm has been implemented in a software package called Copy Number Analyzer for Affymetrix GeneChip Mapping 100K arrays (CNAG). Overall, these enhancements make CNAG a useful tool for high-resolution detection of copy number alterations which can help in the understanding of the pathogenesis of cancers and other diseases as well as in exploring the complexities of the human genome.
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            Genetics of early onset cognitive impairment.

            H Hilger Ropers (2009)
            Intellectual disability (ID) is the leading socio-economic problem of health care, but compared to autism and schizophrenia, it has received very little public attention. Important risk factors for ID are malnutrition, cultural deprivation, poor health care, and parental consanguinity. In the Western world, fetal alcohol exposure is the most common preventable cause. Most severe forms of ID have genetic causes. Cytogenetically detectable and submicroscopic chromosomal rearrangements account for approximately 25% of all cases. X-linked gene defects are responsible in 10-12% of males with ID; to date, 91 of these defects have been identified. In contrast, autosomal gene defects have been largely disregarded, but due to coordinated efforts and the advent of next-generation DNA sequencing, this is about to change. As shown for Fra(X) syndrome, this renewed focus on autosomal gene defects will pave the way for molecular diagnosis and prevention, shed more light on the pathogenesis of ID, and reveal new opportunities for therapy.
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              Subtelomere FISH analysis of 11 688 cases: an evaluation of the frequency and pattern of subtelomere rearrangements in individuals with developmental disabilities.

              P Papenhausen, James Tepperberg, J Ravnan … (2006)
              Subtelomere fluorescence in situ hybridisation (FISH) analysis has increasingly been used as an adjunct to routine cytogenetic testing in order to detect small rearrangements. Previous reports have estimated an overall abnormality rate of 6%, with a range of 2-29% because of different inclusion criteria. This study presents data compiled from 11 688 cases referred for subtelomere FISH testing in three clinical cytogenetic laboratories. In this study population, the detection rate for clinically significant subtelomere abnormalities was approximately 2.5%, with an additional 0.5% detection of presumed familial variants. Approximately half of the clinically significant abnormalities identified were terminal deletions, the majority of which were de novo. Most of the remaining cases were unbalanced translocations between two chromosomes or two arms of the same chromosome. Approximately 60% of the unbalanced translocations were inherited from a parent carrying a balanced form of the rearrangement. Other abnormalities identified included tandem duplications, apparently balanced translocations, partial deletions, and insertions. Interestingly, 9 cases (0.08%) were found to have interstitial deletions of non-telomeric control loci, either BCR on 22q or PML on 15q. The most common clinically significant imbalances found were deletions of 1p, 22q, 4p, 9q, 8p, 2q and 20p. The most common familial variants were a deletion or duplication of 10q, deletion of 4q, deletion of Yq, and duplication of X/Yp onto Xq. This study of subtelomere rearrangements is a 20 fold increase in number over the previously reported largest study and represents an unbiased analysis of subtelomere rearrangements in a large, unselected patient population.
              Article 0 comments Cited 66 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Indian J Hum Genet
                Journal ID (iso-abbrev): Indian J Hum Genet
                Journal ID (publisher-id): IJHG
                Title: Indian Journal of Human Genetics
                Publisher: Medknow Publications & Media Pvt Ltd (India )
                ISSN (Print): 0971-6866
                ISSN (Electronic): 1998-362X
                Publication date (Print): Apr-Jun 2013
                Volume: 19
                Issue: 2
                Pages: 171-178
                Affiliations
                [1 ]Division of Human Genetics, Center for Biomedical Research, Faculty of Medicine Diponegoro University, Semarang, Indonesia
                [2 ]Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
                Author notes
                Address for correspondence: Prof. Sultana M. H. Faradz, MD, PhD, Division of Human Genetics, Center for Biomedical Research, Faculty of Medicine, Diponegoro University, GSG 2 nd Floor, Jl. Dr. Sutomo 14, Semarang, Indonesia. E-mail: sultana@ 123456indosat.net.id
                [*]

                Equal last author

                Article
                Publisher ID: IJHG-19-171
                DOI: 10.4103/0971-6866.116118
                PMC ID: 3758723
                PubMed ID: 24019618
                SO-VID: a67178d7-0075-4f30-bf5b-097fb7cbe45f
                Copyright © Copyright: © Indian Journal of Human Genetics
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Categories
                Subject: Original Article

                ScienceOpen disciplines: Genetics
                Keywords: indonesia,intellectual disability,multiplex ligation dependent probe amplification,subtelomeric rearrangements
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: indonesia, intellectual disability, multiplex ligation dependent probe amplification, subtelomeric rearrangements

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