Plasma cell leukemia (PCL) is a rare lymphoproliferative disorder, accounting for 1-2% of all plasma cell neoplasms, characterized by the presence of >2 × 109/l of plasma cells circulating in the peripheral blood, and exists in two forms: primary PCL (pPCL, 60% of the cases), and secondary PCL (sPCL), the latter being a leukemic transformation in patients with a previously diagnosed multiple myeloma. PCL is an aggressive disease with poor prognosis and a short median survival of 7 months.
Here, we report a pPCL case with hepatosplenomegaly, anemia, thrombocytopenia, fever, fatigue, weight loss, and plasma cell count up to 60% in peripheral blood and 80% in bone marrow. Immunophenotype was compatible with PCL. A del(9)(p22.3) was characterized using banding cytogenetics and array-proven multicolor banding (aMCB), the latter being of enormous significance to characterize breakpoint regions in detail.
To the best of our knowledge, this is the first report of pPCL associated with a partially monosomy 9pter to 9p22.3 as a sole chromosomal abnormality.
Primary plasma cell leukemia; Multiple myeloma; Del(9)(p22.3); Array-proven multicolor banding; Prognostic factors
In assisted reproductive treatments, embryos remaining after fresh embryo transfer are usually selected for cryopreservation based on traditional morphology assessment. Our previous report has demonstrated that array comparative genomic hybridization (aCGH) screening for IVF patients with good prognosis significantly improves clinical and ongoing pregnancy rates in fresh embryo transfer cycles. The current study further investigates the efficiency of applying aCGH in the selection of euploid embryos for cryopreservation as related to pregnancy and implantation outcomes in subsequent frozen embryo transfer (FET) cycles.
First-time IVF patients with good prognosis undergoing fresh single embryo transfer and having at least one remaining blastocyst for cryopreservation were prospectively randomized into two groups: 1) Group A patients had embryos assessed by morphology first and then by aCGH screening of trophectoderm cells and 2) Group B patients had embryos evaluated by morphology alone. All patients had at least one blastocyst available for cryopreservation after fresh embryo transfer. There were 15 patients in Group A and 23 patients in Group B who failed to conceive after fresh embryo transfer and completed the FET cycles. Blastocyst survival and implantation rates were compared between the two groups.
There were no significant differences in blastocyst survival rates between Group A and Group B (90.9% vs. 91.3%, respectively; p >0.05). However, a significantly higher implantation rate was observed in the morphology assessment plus aCGH screening group compared to the morphology assessment alone group (65.0% vs. 33.3%, respectively; p = 0.038). There was no miscarriage observed in Group A while a 16.7% miscarriage rate was recorded in Group B (0% vs. 16.7%, respectively; p >0.05).
While aCGH screening has been recently applied to select euploid blastocysts for fresh transfer in young, low-risk IVF patients, this is the first prospective study on the impact of aCGH specifically on blastocyst survival and implantation outcomes in the subsequent FET cycles of IVF patients with good prognosis. The present study demonstrates that aCGH screening of blastocysts prior to cryopreservation significantly improves implantation rates and may reduce the risk of miscarriage in subsequent FET cycles. Further randomized clinical studies with a larger sample size are needed to validate these preliminary findings.
aCGH; Trophectoderm biopsy; Cryopreservation; Implantation
Van der Woude syndrome is the most common among syndromes which include cleft lip and/or cleft palate as one of the presentations. It is usually caused by mutations in the interferon regulatory factor 6 (IRF6) gene.
We previously reported on a patient with suspected deletion of the IRF6 gene. Using the Affymetrix Human SNP 6.0 Array, the interstitial deletion has been confirmed and found to be approximately 2.327–2.334 Mb within the 1q32.2 region. Although several known genes were deleted, the patient has no other phenotype apart from the orofacial presentations typical of VWS. The same deletion was not present in either parent and his two siblings were also phenotypically normal.
Other than IRF6, the genes which are deleted in this patient appear to be insensitive to copy number and haploinsufficiency. We compared the deletion in this patient with another case which was also mapped by high resolution array but had additional phenotypic features.
1q32; IRF6 gene; Microdeletion; Orofacial clefting; SNP array; Syndromic clefting; Van der Woude syndrome
The reports of 1q25-32 deletion cases are rare. We reported here an 11-year-old Chinese Han female with an interstitial 1q25 deletion displaying mental retardation, clinodactyly of the 5th finger and minor facial anomalies. Notably, the patient did not present growth retardation which is quite common in patients with 1q25-32 deletion encompassing LHX4. The heterozygous deletion in this patient was characterized as 46,XX,del(1)(q25.2-q31.3) with a length of 20.5 Mb according to SNP-array test results. STRP (Short Tandem Repeat Polymorphism) analysis of the family trio indicated the genomic abnormality was de novo with paternal origin. After a genotype-phenotype analysis, we proposed here the loss of a 3.1 Mb critical region including 24 genes within 1q25.2 (chr1:174.5-177.6 Mb, build 36) may account for the mental retardation in patients with 1q25-32 deletion.
Interstitial 1q deletion; SNP-array; Mental retardation; Growth retardation
Partial monosomies of chromosome 16q are rare and overlapping effects from complex chromosomal rearrangements often hamper genotype-phenotype correlations for such imbalances. Here, we report the clinical features of an isolated partial monosomy 16q21q22.1 in a boy with a complex de novo rearrangement possibly resulting from a chromothripsis event.
The patient presented with low birth weight, microcephaly, developmental delay, facial dysmorphisms, short stature, dysmorphic ears and cardiopathy. Standard and molecular cytogenetics showed a complex rearrangement characterised by a pericentromeric inversion in one of chromosomes 12 and an inverted insertional translocation of the 12q14q21.1 region, from the rearranged chromosome 12, into the q21q22.1 tract of a chromosome 16. Array-CGH analysis unravelled a partial 16q21q22.1 monosomy, localised in the rearranged chromosome 16.
The comparison of the present case to other 16q21q22 monosomies contributed to narrow down the critical region for cardiac anomalies in the 16q22 deletion syndrome. However, more cases, well characterised both for phenotypic signs and genomic details, are needed to further restrict candidate regions for phenotypic signs in 16q deletions. The present case also provided evidence that a very complex rearrangement, possibly caused by a chromothripsis event, might be hidden behind a classical phenotype that is specific for a syndrome.
Complex insertional translocation; Chromothripsis; Array-CGH; Developmental and growth delay; Dysmorphic features; Partial monosomy 16q21q22.1; Congenital heart defects
The association of microRNA alterations with progression and treatment outcome has been revealed in different types of cancers. To find miRNAs involved in imatinib response we performed miRNA microarray followed by RT-qPCR verification of 9 available diagnostic bone marrow core biopsies from 9 CML patients including 4 imatinib-resistant and 5 imatinib-responder patients. Only one differentially expressed miRNA, miR-181c, was found when the imatinib-resistant group was compared with imatinib-responders. Significant down-regulation of miR-181c in imatinib-resistant versus imatinib-responders was confirmed by qRT-PCR. Some miR-181c target genes such as PBX3, HSP90B1, NMT2 and RAD21 have been associated with drug response.
miRNA; CML; Imatinib response
To expose the unusual nature of a coincident sex chromosomal aneuploidy in a patient and his father. Molecular mechanisms involved probably are based on the sperm chromosome of paternal origin, which determine the mode of formation. Conventional cytogenetics techniques and multiple Quantitative Fluorescent PCR of STR markers in sexual chromosomes in the patient and his parents.
48,XXYY and 47,XYY aneuploidies in the patient and his father, respectively, were identified. The additional X and Y chromosomes showed parental origin.
An infrequent origin of the 48,XXYY syndrome was demonstrated. Mostly, it is thought to result from an aneuploid sperm produced through two consecutive non disjunction events in both meiosis I and II in a chromosomally normal father, but in our father’s patient a 47,XYY was discovered. It is suggested that a higher incidence of 24,XY and 24,YY sperm may be possible in 47,XYY individuals andan increased risk for aneuploidy pregnancies may exist. Although 48,XXYY patients and Klinefelter syndrome are often compared, recently they are regarded as a distinct genetic and clinical entity.
48,XXYY; 47,XYY; Mechanism origin; Paternal; Spermatogenesis
RBFOX1 is an important splicing factor regulating developmental and tissue-specific alternative splicing in heart, muscle, and neuronal tissues. Constitutional genetic defects in RBFOX1 are implicated in multiple medical conditions.
We identified 14 copy number variants (CNV) involving RBFOX1 from 2,124 consecutive pediatric patients referred for chromosomal microarray analysis (CMA), including 13 intragenic deletions and a single intragenic duplication. The clinical significances of the intragenic deletions of RBFOX1 were evaluated.
Our data strongly supports the associations of intragenic deletions of RBFOX1 with a diversity of neurodevelopmental and neuropsychiatric disorders, and possibly other clinical features.
Microdeletion; Chromosome 16p13.3; RBFOX1; Chromosomal microarray analysis (CMA); Seizures; Developmental delay
Exact breakpoint determination by oligonucleotide array-CGH has improved the analysis of genotype-phenotype correlations in cases with chromosome aberrations allowing a more accurate definition of relevant genes, particularly their isolated or combined impact on the phenotype in an unbalanced state. Chromosomal imbalances have been identified as one of the major causes of mental retardation and/or malformation syndromes and they are observed in ~2-5% of the cases. Here we report a female child born to non-consanguineous parents and having multiple congenital anomalies such as atrial septal defect and multiple ventricular septal defects, convergent strabismus, micropthalmia, seizures and mental retardation, with her head circumference and stature normal for her age. Cytogenetic study suggested 46,XX,add(8)(p23). Further analysis by array-CGH using 44K oligonucleotide probe confirmed deletion on 8p23.3p23.1 of 7.1 Mb and duplication involving 15q23q26.3 of 30 Mb size leading to 46,XX,der(8)t(8;15)(p23.3;q23)pat.arr 8p23.3p23.1(191,530-7,303,237)x1,15q23q26.3(72,338,961-102,35,195)x3. The unique phenotypic presentation in our case may have resulted from either loss or gain of a series of contiguous genes which may have resulted in a direct phenotypic effect and/or caused a genetic regulatory disturbance. Double segmental aberrations may have conferred phenotypic variability, as in our case, making it difficult to predict the characteristics that evolved as a result of the global gene imbalance, caused by the concomitant deletion and duplication.
Chromosomal imbalance; 8p23 deletion; 15q23 duplication; IGF1R; GATA4; MCPH1
Deletions of the gene encoding mediator subcomplex 12 (MED12) in human smooth muscle tumors rank among the most frequent genomic alterations in human tumors at all. In a minority of these cases, small deletions are found. In an attempt to delineate key features of the deletions aimed at a better understanding of the molecular pathogenesis of uterine smooth muscle tumors we have analyzed 70 MED12 deletions including 46 cases from the literature and 24 own unpublished cases.
The average length of the deletions was 18.7 bp ranging between 2 bp and 43 bp. While in general multitudes of 3 clearly dominated leaving the transcript in frame, deletions of 21, 24, 30, and 33 nucleotides were clearly underrepresented. Within the DNA segment affected deletion breakpoints were not randomly distributed. Most breakpoints clustered within the center of the segment where two peaks of breakpoint clusters could be distinguished. Interestingly, one of these clusters coincides with the loop of a putative folded non-B DNA structure whereas a much lower number of breaks noted in the 5′ and 3′ stem of the structure forming an intramolecular B-helix. The second cluster mainly consisting of 3′ breaks was located in a region downstream adjacent to the stem.
The present study describes for the first time main characteristics of MED12 deletions occurring in smooth muscle tumors. Interestingly, the non-random distribution of breakpoints within the deletion hotspot region may point to a role of non-canonical DNA structures for the occurrence of these mutations and the molecular pathogenesis of uterine smooth muscle tumors, respectively.
Deletions; Smooth muscle tumors; MED12; Non-canonical DNA-structures
Chromosomal abnormalities are common in embryos produced in vitro and cause implantation failure, miscarriage, and serious medical problems in infants. Because preimplantation genetic screening (PGS) is increasingly being used to detect aneuploidy in embryos with the purpose of improving implantation rates after IVF (in vitro fertilization), we aimed to validate the usefulness of array CGH for the preimplantation genetic screening (PGS) of embryos at the blastocyst stage of development.
A total of 150 blastocysts were biopsied from couples undergoing IVF and analyzed using array CGH. We found that 54.5% (73/134) of the blastocysts were euploid embryos, whereas 45.5% of the embryos (61/134) had chromosomal abnormalities. Multiple chromosome abnormality was most frequently observed (34.4%), and dual aneuploidy was observed in 26.2% of the embryos. Monosomy (21.3%) appeared more frequently than trisomy (18%).
Chromosomal microarray analysis provided clinically significant cytogenetic information regarding the frequency and variety of chromosomal abnormalities observed in embryos at the blastocyst stage, suggesting that this is a useful tool for comprehensive aneuploidy screening in IVF.
Array comparative genomic hybridization (CGH) is a powerful tool for detecting unbalanced chromosomal alterations. To validate the usefulness of array CGH in newborn screening, we examined 20,126 unselected infants. In addition, the number of newborns analyzed with array CGH is the largest one ever reported.
A total of 20,126 unselected newborns were investigated with array CGH and cytogenetic analyses. The analyses revealed 87 cases with chromosome abnormalities. Of these, 53 cases had significant chromosome aneuploidies, including trisomy 13, trisomy 21, 47,XXY or 45,X, and the other 34 cases presented partial chromosomal deletions or duplications.
In this study, we show that array CGH is an appropriate tool for the screening of chromosomal abnormalities in newborns, especially for the infants without distinct clinical features.
Array CGH; Newborns; Chromosome abnormality
Hearing loss is the most common birth defect and the most prevalent sensorineural disorder in developed countries. More than 50% of prelingual deafness is genetic, most often autosomal recessive and nonsyndromic, of which 50% can be attributed to the disorder DFNB1, caused by mutations in GJB2 and GJB6. Sensorineural hearing loss and male infertility (Deafness-Infertility Syndrome; DIS) is a contiguous gene deletion syndrome resulting from homozygous deletion of the CATSPER2 and STRC genes on chromosome 15q15.3. Females with DIS have only hearing loss and are fertile. Until recently this syndrome has only been described in three consanguineous families and 2 nonconsanguineous families.
We recently indentified a patient with hearing loss and macrocephaly who was found to be homozygous for this deletion. Her nonconsanguineous parents are both carriers. We examined our database of patients tested by array CGH and determined that just over 1% of our patients are heterozygous for this deletion. If this number is representative of the general population, this implies a 1% carrier frequency and prevalence of DIS of 1 in 40,000 individuals.
We propose that DIS is a greatly under-diagnosed cause of deafness and should be considered in children with hearing loss. Likewise, current molecular genetic testing panels for hearing loss in the United States should be expanded to include deletion/duplication analysis of this region.
Deafness-Infertility Syndrome; CATSPER2; STRC; Array CGH
Acute myelogeneous leukemia (AML) is a malignancy of the hematopoietic stem cells, for which cytogenetic analysis is still one of the most important diagnostic and prognostic tools. Still, we are far away from having seen and described all possible genetic changes associated with this kind of acquired disease.
Bone marrow cells of a female patient with clinical diagnoses of AML and immunophenotypically confirmed AML-M4 were studied by GTG-banding. The later was not able to resolve all karyotypic changes and the complex karyotype was characterized in more detail by fluorescence in situ hybridization (FISH) and array-proven multicolor banding (aMCB). To the best of our knowledge, the present case is the only one ever seen with a del(5)(q14q34), a der(17)t(4;17)(p13;p13), a del(2)(p23), a der(4)t(4;7)(p13;q11.23), a der(22)t(11;22)(q23;q11.2) and two complex rearranged chromosomes 11 involving chromosomes 7 and 22 as well as 2.
The yet unreported breakpoints observed in this case seem to be correlated with an adverse prognosis. Overall, molecular cytogenetic studies are suited best for identification and characterization of chromosomal rearrangements in acute leukemia and single case reports as well as large scale studies are necessary to provide further insides in karyotypic changes taking place in human malignancies.
Acute myeloid leukemia (AML); Chromosomal abnormalities; Fluorescence in situ hybridization (FISH); Array-proven multicolor banding (aMCB)
The editors of Molecular Cytogenetics would like to thank all our reviewers who have contributed to the journal in volume 5 (2012).
Array CGH is widely used in cytogenetics centres for postnatal constitutional genome analysis, and is now recommended as a first line test in place of G-banded chromosome analysis. At our centre, first line testing by oligonucleotide array CGH for all constitutional referrals for genome imbalance has been in place since June 2008, using a patient vs patient hybridisation strategy to minimise costs.
Out of a total of 13,412 patients tested with array CGH, 8,794 (66%) had array CGH as the first line test. Referral indications for this first line group ranged from neonatal congenital anomalies through to adult neurodisabilities; 25% of these patients had CNVs either in known pathogenic regions or in other regions where imbalances have not been reported in the normal population. Of these CNVs, 46% were deletions or nullisomy, 53% were duplications or triplications, and mosaic imbalances made up the remainder; 87% were <5Mb and would likely not be detected by G-banded chromosome analysis. For cases with completed inheritance studies, 20% of imbalances were de novo.
Array CGH is a robust and cost-effective alternative to traditional cytogenetic methodology; it provides a higher diagnostic detection rate than G-banded chromosome analysis, and adds to the sum of information and understanding of the role of genomic imbalance in disease. Use of novel hybridisation strategies can reduce costs, allowing more widespread testing.
Array CGH; First line testing; G-banded karyotype analysis; CNV
Triplication is a rare chromosomal anomaly. We identified a de novo triplication of 11q12.3 in a patient with developmental delay, distinctive facial features, and others. In the present study, we discuss the mechanism of triplications that are not embedded within duplications and potential genes which may contribute to the phenotype.
The identified triplication of 11q12.3 was 557 kb long and not embedded within the duplicated regions. The aberrant region was overlapped with the segment reported to be duplicated in 2 other patients. The common phenotypic features in the present patient and the previously reported patient were brain developmental delay, finger abnormalities (including arachnodactuly, camptodactyly, brachydactyly, clinodactyly, and broad thumbs), and preauricular pits.
Triplications that are not embedded within duplicated regions are rare and sometimes observed as the consequence of non-allelic homologous recombination. The de novo triplication identified in the present study is novel and not embedded within the duplicated region. In the 11q12.3 region, many copy number variations were observed in the database. This may be the trigger of this rare triplication. Because the shortest region of overlap contained 2 candidate genes, STX5 and CHRM1, which show some relevance to neuronal functions, we believe that the genomic copy number gains of these genes may be responsible for the neurological features seen in these patients.
Triplication; STX5; CHRM1; 11q12.3; Developmental delay
Heterochromatic variants of pericentromere of chromosome 9 are reported and discussed since decades concerning their detailed structure and clinical meaning. However, detailed studies are scarce. Thus, here we provide the largest ever done molecular cytogenetic research based on >300 chromosome 9 heteromorphism carriers.
In this study, 334 carriers of heterochromatic variants of chromosome 9 were included, being 192 patients from Western Europe and the remainder from Easter-European origin. A 3-color-fluorescence in situ hybridization (FISH) probe-set directed against for 9p12 to 9q13~21.1 (9het-mix) and 8 different locus-specific probes were applied for their characterization. The 9het-mix enables the characterization of 21 of the yet known 24 chromosome 9 heteromorphic patterns. In this study, 17 different variants were detected including five yet unreported; the most frequent were pericentric inversions (49.4%) followed by 9qh-variants (23.9%), variants of 9ph (11.4%), cenh (8.2%), and dicentric- (3.8%) and duplication-variants (3.3%). For reasons of simplicity, a new short nomenclature for the yet reported 24 heteromorphic patterns of chromosome 9 is suggested. Six breakpoints involved in four of the 24 variants could be narrowed down using locus-specific probes.
Based on this largest study ever done in carriers of chromosome 9 heteromorphisms, three of the 24 detailed variants were more frequently observed in Western than in Eastern Europe. Besides, there is no clear evidence that infertility is linked to any of the 24 chromosome 9 heteromorphic variants.
Chromosome 9; Heteromorphism; Breakpoints; Western Europe; Eastern Europe
Nowadays, the genus Bryconamericus is placed in subfamily Stevardiinae within of Characidae, but not shows consistent evidence of monophyletism. The purpose of this work was to study the chromosomes of three species of Bryconamericus, aiming to add cytogenetic knowledge and contribute to the understanding of the chromosomal evolution of this genus.
The chromosomes of three species of Bryconamericus were analyzed using cytogenetic techniques. The karyotype of Bryconamericus stramineus contained 6 metacentric (m) + 10 submetacentric (sm) + 16 subtelocentric (st) + 20 acrocentric (a), the fundamental number (FN) of 84, one silver impregnated (Ag-NOR) pair, one pair bearing the 18S ribosomal DNA sites, another pair bearing the 5S rDNA sites, and a few positive C-bands. Bryconamericus turiuba had a karyotype containing 8 m + 10sm + 14st + 20a (FN = 84), one chromosome pair Ag-NOR, two pairs bearing the 18S rDNA sites, two pairs bearing the 5S rDNA sites, and a few C-band regions. Bryconamericus cf. iheringii had a karyotype containing 10 m + 14sm + 18st + 10a (FN = 94), including one pair with a secondary constriction Ag-NOR positive. In this karyotype the fluorescent in situ hybridization (FISH) showed the 18S and 5S rDNA probe in adjacent position.
The results obtained in this work showed different characteristics in the organization of two multigene families, indicating that distinct evolutionary forces acting on the diversity of rDNA sequences in the genome of three Bryconamericus species.
Chromosomes; Heterochromatin; NOR; FISH; rDNA probe
Despite the theoretical and experimental progress, our understanding on sex chromosome differentiation is still diagrammatic. The accumulation of repetitive DNA sequences is believed to occur in early stages of such differentiation. As fish species present a wide range of sex chromosome systems they are excellent models to examine the differentiation of these chromosomes. In the present study, the chromosomal distribution of 9 mono-, di- and tri-nucleotide microsatellites were analyzed using fluorescence in situ hybrization (FISH) in rock bream fish (Oplegnathus fasciatus), which is characterized by an X1X2Y sex chromosome system. Generally, the males and females exhibited the same autosomal pattern of distribution for a specific microsatellite probe. The male specific Y chromosome displays a specific amount of distinct microsatellites repeats along both arms. However, the accumulation of these repetitive sequences was not accompanied by a huge heterochromatinization process. The present data provide new insights into the chromosomal constitution of the multiple sex chromosomes and allow further investigations on the true role of the microsatellite repeats in the differentiation process of this sex system.
Oplegnatidae; X1X2Y sex chromosomes; Fluorescence in situ hybridization; Repetitive DNAs; Chromosomal differentiation
Karyotyping is considered the gold standard for the genome-wide detection of genomic imbalances in prenatal diagnosis, but it has a number of inherent limitations, namely the time required to culture cell and the limited resolution(5 ~ 10 Mb). Although fluorescence in situ hybridization (FISH) can also be used as a rapid prenatal diagnosis for common aneuploidies, it is labor intensive, requires prior knowledge of the regions of interest, and can only be used to diagnose one or a few genomic regions simultaneously. Array comparative genomic hybridization (aCGH) can overcome the resolution, the locus-specific, and the time limitations of the karyotyping and FISH techniques and is currently the most powerful method for detecting chromosomal alterations in pre and postnatal clinical cases. Several investigations have suggested that the aCGH testing should be considered a first-tier test for the diagnosis of cytogenetic aberrations in the fetus.
This study used karyotyping, FISH, sequence-tagged site (STS) analysis and aCGH to diagnose a case of de novo duplication of chromosome 21q22.12 → q22.3 with other concomitant deletion and duplication of small fragments in 21q associated with Down syndrome prenatally.
FISH, aCGH and STS analysis are useful in prenatal investigation of the nature of de novo alterations of small fragments of the chromosome.
Array comparative genomic hybridization (aCGH); Fluorescence in situ hybridization (FISH); Sequence-tagged site (STS); Partial duplication; Prenatal diagnosis; Down syndrome
The ultimate goal of human genetics is to understand the role of genome variation in elucidating human traits and diseases. Besides single nucleotide polymorphism (SNP), copy number variation (CNV), defined as gains or losses of a DNA segment larger than 1 kb, has recently emerged as an important tool in understanding heritable source of human genomic differences. It has been shown to contribute to genetic susceptibility of various common and complex diseases. Despite a handful of publications, its role in cardiovascular diseases remains largely unknown. Here, we deliberate on the currently available technologies for CNV detection. The possible utility and the potential roles of CNV in exploring the mechanisms of cardiac remodeling in hypertension will also be addressed. Finally, we discuss the challenges for investigations of CNV in cardiovascular diseases and its possible implications in diagnosis of hypertension-related left ventricular hypertrophy (LVH).
Copy number variation; Genetic susceptibility; Hypertension; Left ventricular hypertrophy
Array based comparative genomic hybridization (arrayCGH) has been increasingly used as the method of choice for diagnosis of patients with unexplained developmental delay/intellectual disability (DD/ID) but is not universally available for the high throughput use in routine practice. The next-generation sequencing (NGS) techniques, emerging as a new tool in clinical diagnostics, are at present quite labour-intensive and expensive. Since multiplex ligation-dependent probe amplification (MLPA) is relatively fast, easily interpreted and cost-effective, it is still a method of choice for screening large cohorts of patients with DD/ID.
We prospectively studied a cohort of 150 patients with DD/ID with or without dysmorphic features or additional congenital abnormalities. We used two distinct MLPA kits, SALSA P036 and P070, for subtelomere screening and MLPA kit SALSA P245 for the 21 common microdeletion syndromes. Subtelomere analysis was performed by both kits in all patients. All imbalances were verified by follow-up MLPA kits. The MLPA analysis revealed chromosome aberrations in 21 (14%) cases: 11 subtelomeric rearrangements and 10 microdeletions.
We have presented the results of the investigation of patients with DD/ID obtained by using a combination of the MLPA sets for subtelomere aberrations and microdeletion syndromes followed by the confirmation of the aberrant results by the region-specific MLPA kits. The use of two subtelomeric kits per patient and investigation of all aberrations by follow-up sets has reduced the rate of false positive and negative results and improved the diagnostic yield. The relatively low cost, simplicity and reliability makes MLPA an effective first-tier cytogenetic diagnostic test for screening large cohorts of DD/ID patients.
Intellectual disability; Chromosome aberrations; Genetic testing; Developing countries