Role of Interphase FISH Assay on Air-Dried Smears in Identifying Specific Structural Chromosomal Abnormalities among Pediatric Patients with Acute Leukemias

Leukemia-associated structural chromosomal abnormalities (SCA) can be identified either by karyotyping or interphase-fluorescence in-situ hybridization (i-FISH) assays. Both karyotyping and i-FISH on mononuclear cell suspension are time, resource, and manpower-consuming assays. In this study, we have compared the results of specific leukemia-associated SCAs identified by i-FISH on air-dried bone marrow (BM)/peripheral blood (PB) smears and BM karyotyping. The study was conducted among pediatric patients (age ≤ 18 years) diagnosed with acute leukemias between January 2018 to December 2022. The results of i-FISH on air-dried BM/PB smears and BM-karyotyping for our SCA of interest (BCR::ABL1, ETV6::RUNX1, TCF3::PBX1, KMT2A rearrangement, RUNX1::RUNX1T1, CBFB::MYH11, and PML::RARA) were entered in a contingency table and the agreement of results was calculated. The strength of agreement was assessed by Cramer's V test. Among 270 patients, SCA of interest was identified among 26% and 17% of patients by i-FISH on air-dried smears and karyotyping, respectively. Excluding 53 patients with metaphase failure, the remaining 217 patients had 92% agreement (Cramer's V of 0.931 with p < 0.000) between the results for specific SCAs identified by both techniques. On excluding samples with cryptic cytogenetic aberrancies, there was 99% agreement (Cramer's V of 0.953 with p < 0.000) for gross SCA identified by both techniques. In addition, i-FISH on air-dried smears identified SCA in 30% of patients with metaphase failure. I-FISH on air-dried PB/BMA smears is a less-labor and  resource-consuming assay. It can be considered an efficient alternative to conventional karyotyping for  identifying specific SCA of interest in under-resourced laboratories.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12288-023-01699-2.

The potential influence of GSTT1 null genetic polymorphism on coronary artery disease: A pilot study in a South Indian cohort

BACKGROUND

Indians are known to have the highest rates of coronary artery disease (CAD), with the conventional risk factors failing to explain the increased risk. Possible candidate genes to study both the environmental and genetic risk associated with CAD is the glutathione S-transferase (GST) family, as it is involved in detoxification.

METHODS

This case-control assessed the association between GSTM1 and GSTT1 polymorphisms in Indian patients with CAD. Fifty patients with CAD and 50 healthy volunteers were genotyped for the two polymorphisms by polymerase chain reaction. The genotype frequencies between the groups were compared, where a p-value of less than 0.05 was considered as statistically significant.

RESULTS

There was a significant inverse association between GSTT1 null polymorphism and CAD susceptibility.

Risk association of the nitric oxide synthase VNTR intron 4 a/b variant with diabetic nephropathy - a pilot study

Diabetic nephropathy (DN) is known to be a leading complication of type 2 diabetes mellitus (T2D). This study evaluated whether the VNTR intron 4 a/b and rs1799983 polymorphisms of endothelial-derived nitric oxide synthase (eNOS) gene modulated the risk of developing DN in Asian Indian patients. The eNOS variants were genotyped in 200 patients, 100 with DN and 100 without DN. A significant risk association was observed for the VNTR intron 4 a/b (p < 0.05). Haplotype analysis revealed that the allele combination of rs1799983894 G/Intron 4b and rs1799983894 T/Intron 4b had a statistically significant inverse association with DN.

Candidate Gene Expression in Regional Population and Its Relevance for Radiation Triage

Quantification of gene expression signatures has been substantiated as a potential and rapid marker for radiation triage and biodosimetry during nuclear emergencies. Similar to the established biodosimetry assays, the gene expression assay has drawbacks such as being highly dynamic and transient, not specific to ionizing radiation, and also influenced by confounding factors such as gender, health status, lifestyle, and inflammation. In view of that, prior knowledge of baseline expression of certain candidate genes in a population could complement the discrimination of the unexposed from the exposed individuals without the need for individual pre-exposure controls. We intended to establish a baseline expression of reported radiation-responsive genes such as CDKN1A, DDB2, FDXR, and PCNA in the blood samples of healthy human participants and then compare it with diabetic/hypertension participants (as a chronic inflammatory condition) drawn from south Indian population. Further, we have examined the appropriateness of the assay for radiation triage-like situations; i.e., the expression profiles of those genes were examined in the participants who underwent X-ray-based medical imaging. Acute inflammation induced by lipopolysaccharide exposure in the blood significantly increased the fold expression of those genes (p < 0.0001) compared to the control. Whereas the basal expression level of those genes among the participants with the inflammatory condition is marginally higher than those observed in the healthy participants; despite the excess, the fold increase in those genes between the groups did not differ significantly. Consistent with the inflammatory participants, the basal expression level of those genes in the blood sample of participants who received X-radiation during neuro-interventional and computed tomography imaging is marginally higher than those observed in the pre-exposure of respective groups. Nevertheless, the fold increase in those genes did not differ significantly as the fold change fell within the two folds. Thus, overall results suggest that the utility of CDKN1A, DDB2, FDXR, and PCNA gene expression for radiation triage specific after very low-dose radiation exposure needs to be interpreted with caution for a much more reliable triage.

Mercaptopurine induced myelosuppression in a child with a NUDT15 rs116855232 homozygous variant

Introduction

Mercaptopurine (6-MP) is the backbone of the consolidation and maintenance therapy for paediatric acute lymphoblastic leukaemia (ALL). Nevertheless, it can cause critical myelosuppression. Predicting adverse reactions to 6-MP often involves the investigation of pharmacogenetic variants; in particular thiopurine S-methyltransferase ( TPMT) and nudix hydrolase 15 ( NUDT15). Lately, NUDT15 variants have been shown to play a significant pharmacogenetic role in predicting 6-MP intolerance in children of Asian descent.

Case Report

We present a six-year-old male child of Indian origin with persistent cytopenia after treatment. This prompted targeted sequencing of the genes TPMT and NUD15. The results revealed two copies of the variant of NUD15 rs116855232, that is, NUDT15*2 genotype.

Management and Outcome

Since the NUDT15*2 allele classified the patient as a poor metabolizer, he was restarted on a low dose of 6-MP, which he tolerated.

Discussion

Individuals with the NUDT15*2allele (*2/*2 genotype) are poor metabolizers of thiopurines which results in an adverse reaction to 6-MP. About 3.5% of Indians show variations in the TPMT gene as compared to 19.4% variations observed in NUDT15, which makes the latter a more reliable disease marker.

Burden of Type 2 Diabetes and Associated Cardiometabolic Traits and Their Heritability Estimates in Endogamous Ethnic Groups of India: Findings From the INDIGENIUS Consortium

To assess the burden of type 2 diabetes (T2D) and its genetic profile in endogamous populations of India given the paucity of data, we aimed to determine the prevalence of T2D and estimate its heritability using family-based cohorts from three distinct Endogamous Ethnic Groups (EEGs) representing Northern (Rajasthan [Agarwals: AG]) and Southern (Tamil Nadu [Chettiars: CH] and Andhra Pradesh [Reddys: RE]) states of India. For comparison, family-based data collected previously from another North Indian Punjabi Sikh (SI) EEG was used. In addition, we examined various T2D-related cardiometabolic traits and determined their heritabilities. These studies were conducted as part of the Indian Diabetes Genetic Studies in collaboration with US (INDIGENIUS) Consortium. The pedigree, demographic, phenotypic, covariate data and samples were collected from the CH, AG, and RE EEGs. The status of T2D was defined by ADA guidelines (fasting glucose ≥ 126 mg/dl or HbA1c ≥ 6.5% and/or use of diabetes medication/history). The prevalence of T2D in CH (N = 517, families = 21, mean age = 47y, mean BMI = 27), AG (N = 530, Families = 25, mean age = 43y, mean BMI = 27), and RE (N = 500, Families = 22, mean age = 46y, mean BMI = 27) was found to be 33%, 37%, and 36%, respectively, Also, the study participants from these EEGs were found to be at increased cardiometabolic risk (e.g., obesity and prediabetes). Similar characteristics for the SI EEG (N = 1,260, Families = 324, Age = 51y, BMI = 27, T2D = 75%) were obtained previously. We used the variance components approach to carry out genetic analyses after adjusting for covariate effects. The heritability (h²) estimates of T2D in the CH, RE, SI, and AG were found to be 30%, 46%, 54%, and 82% respectively, and statistically significant (P ≤ 0.05). Other T2D related traits (e.g., BMI, lipids, blood pressure) in AG, CH, and RE EEGs exhibited strong additive genetic influences (h² range: 17% [triglycerides/AG and hs-CRP/RE] - 86% [glucose/non-T2D/AG]). Our findings highlight the high burden of T2D in Indian EEGs with significant and differential additive genetic influences on T2D and related traits.

DHEA and polycystic ovarian syndrome: Meta-analysis of case-control studies

BACKGROUND

Polycystic ovarian syndrome is a heterogenous endocrine disorder characterized by irregular menstrual cycles, hirsuitism and polycystic ovaries. It is further complicated by metabolic syndrome, infertility and psychological stress. Although the etiopathogenesis is unclear, many studies have pointed out the role of stress in this syndrome. DHEA, being a stress marker is being used by scientists to compare the stress levels between polycystic ovarian cases and healthy controls. However, the results obtained from previous studies are equivocal.

OBJECTIVE

To perform meta-analysis and find the association between stress and the syndrome.

DATA SOURCES

Relevant data till January 2021 were retrieved from PubMed, Scopus, Embase and Web of Science using MeSH terms.

STUDY SELECTION

Case-control studies having PCOS subjects as cases and healthy women as controls were selected provided; their basal DHEA levels were mentioned in the published articles.

DATA EXTRACTION

Two authors independently extracted the articles and qualified the final studies.

DATA SYNTHESI

Pooled meta-analysis was done using random effect model and showed level of DHEA statistically significant in PCOS compared to healthy controls (SMD = 1.15, 95% CI = 0.59-1.71).Heterogeneity was statistically significant as well (I2 = 95%).

CONCLUSION

Thismeta-analysis on DHEA and PCOS has helped in generating evidence regarding the involvement of stress in the pathogenesis of PCOS.

Cortisol and polycystic ovarian syndrome - a systematic search and meta-analysis of case-control studies

BACKGROUND

Polycystic ovarian syndrome (PCOS) has become an emerging disorder affecting women of reproductive age group. Its intricate presentation of signs and symptoms makes it a disease of interest to research. While there are varied hypotheses related to its cause and pathogenesis, role of stress in this disease is yet to be grounded. There is emerging body of evidence on cortisol and PCOS, although it is currently equivocal.

METHODS

Medline, Embase, Pubmed, Science Direct, Google Scholar, and Scopus were searched from March 1985 to March 2020 using MeSH terms. After dual quality assessments and data abstraction, the final articles were included for meta-analysis.

RESULTS

Forty-one studies qualified for the analysis. Pooled meta-analysis showed that the level of cortisol was significantly higher in PCOS when compared to healthy controls (standard mean difference [SMD] = 0.83, 95% confidence interval [CI] = 0.42-1.23) with highly significant heterogeneity (I² = 94%). Subgroup analysis done based on type of sample stated high effect size for blood cortisol levels (SMD = 0.9, 95%CI = 0.32; 1.51) compared to overall effect.

CONCLUSIONS

This systematic review and meta-analysis on cortisol and PCOS have helped in generating evidence regarding the role of cortisol in the pathogenesis of PCOS and the use of cortisol estimation as a potential stress marker in PCOS.

Cytogenetic and Fluorescence in situ Hybridization Profile of Pediatric Acute Lymphoblastic Leukemia in a University Hospital in South India

OBJECTIVE

The purpose of this study was to evaluate the cytogenetic and fluorescent in situ hybridization (FISH) profile in children with acute lymphoblastic leukemia (ALL), referred to a university hospital in a 5-year 6-month period.

SUBJECTS AND METHODS

Cytogenetic analysis of the bone marrow aspirate specimens of 91 patients was performed by standard Giemsa (G)-banding and interphase FISH (iFISH).

RESULTS

The frequency of chromosomal abnormalities detected by G-banding was 29.5%, and the frequency of nonrandom abnormalities with independent prognostic significance identified by iFISH was 46.4%. The abnormality with the highest frequency was gain of RUNX1 (n = 18, 21.4%), followed by ETV6/RUNX1 fusion (n = 7, 8.3%), and gain of KMT2A (n = 6, 7.1%). Additionally, rarely reported gains of ETV6, PBX1, and ABL1 were observed at a frequency of 6% (n = 5), and the deletion of ETV6 and TCF3 was seen at a frequency of 3.6% (n = 3) and 2.3% (n = 2), respectively. A 10-year old with intrachromosomal amplification of chromosome 21 was also observed.

CONCLUSIONS

This study strengthens and widens the current knowledge of the cytogenetic landscape of pediatric ALL.

Blast size-specific flowcytometric ploidy assessment using FxCycleTM Violet dye and its correlation with conventional cytogenetic ploidy in pediatric precursor B-lineage acute lymphoblastic leukemia patients

INTRODUCTION

Numerical chromosomal abnormalities (aneuploidies), present in approximately 30%-50% of pediatric precursor B-lineage acute lymphoblastic leukemia (B-ALL) patients, are commonly identified through a laborious conventional cytogenetic (CG) technique. Flow cytometry (FCM) can identify both physical and fluorescent properties of cells together, and by using fluorescent nucleic-acid-binding dyes, FCM can identify variations in total nucleic-acid content of cells. FxCycle^TM Violet dye (FxCV) is a selective DNA-binding dye which permits simultaneous multiparametric immunophenotyping and cell-cycle/ploidy assessment in a single assay. To date, only two studies have demonstrated the feasibility of FxCV-aided FCM-ploidy analysis in B-ALL patients and only one of these studies have compared their results with CG-ploidy.

METHODOLOGY

Blast size-specific FCM-ploidy was prospectively analyzed using FxCV-dye in 109 pediatric B-ALL patients, and the results were compared with concurrent CG-ploidy status.

RESULTS

FCM-ploidy categorization was feasible in 98% of samples tested and the results were 82% concordant with CG-ploidy status. We observed significant correlation between DNA content and blast size (r = .823, P < .001) and could demonstrate size differences between diploid vs low-hyperdiploid (P = .025), diploid vs high-hyperdiploid (P < .001) and low- vs high-hyperdiploid blasts (P = .007).

CONCLUSION

FCM-ploidy assessment using FxCV dye is a reliable assay and the results closely concur with CG-based ploidy stratification and risk assessment. Using blast size-assisted DNA content analysis, the results of FCM-ploidy analysis can be further fine-tuned.

A case-control association of RANTES (-28C >G) and CCR5-Delta32 polymorphisms with Parkinson's disease in Indians

Recent studies have suggested that chemokines and their receptors are involved in several neurodegenerative disorders. Also, numerous lines of evidence have indicated that inflammatory processes are involved in the pathogenesis of Parkinson's disease (PD). We have examined whether single nucleotide polymorphisms at the genes encoding chemokines RANTES (-28 C > G), RANTES (-403 A > G) MCP-1 (-2518 A > G), and chemokine receptors CCR2 (+190 G > A) and CCR5 (-Δ32) were associated with sporadic PD risk in the Indian population. This pilot case-control association study included 97 PD patients and 100 control subjects, who were all genotyped with PCR-RFLP for the five polymorphisms. There was no statistically significant difference in the genotype frequencies between the cases and controls for the MCP1 (-2518 A > G), RANTES (-403 A > G) and CCR2 (+190 G > A) polymorphisms. However, the results revealed a significant difference in the frequency of the heterozygous CG genotype for the RANTES (-28 C > G) polymorphism (OR = 0.49, p = 0.03) between the cases and controls. A negative association was demonstrated in the dominant model where, compared with the GG genotype, a higher frequency of the GC + CC genotype was observed in the controls. Also, a statistically significant higher frequency of the CCR5 heterozygous genotype WT/Δ32 in the controls was observed (OR = 0.31, p = 0.04). Combined genotype analysis revealed that the allele combination of G-A-G-C of CCR2 (+190G > A), MCP-1 (-2518 A/G), RANTES (-403 A/G) and RANTES (-28 C/G) respectively had a risk association with PD (OR = 6.18, p = 0.005).

Clinical, biochemical and genetic characteristics of children with congenital adrenal hyperplasia due to 17α-hydroxylase deficiency

Objectives Congenital adrenal hyperplasia (CAH) is an autosomal recessive disorder, that could rarely be due to 17 α-hydroxylase deficiency (17αOHD) and/or 17,20 lyase deficiency. Mutation of CYP17A1 gene causes deficiency of glucocorticoids and androgens but excess of mineralocorticoids. Lack of genital ambiguity in most children causes a delay in diagnosis even until puberty. Classical presentation with hypertension and hypokalemia is often not encountered. We intended to study the clinical, biochemical and genetic characteristics of children diagnosed with CAH due to 17αOHD. Methods Three children who were diagnosed with CAH due to 17αOHD in our institute and on follow up were included in this retrospective study. Clinical, biochemical and genetic characteristics of these children were retrieved and studied from electronic medical records. Results Two children were genetic females and one was genetic male, but all three were raised as females. All had hypertension at diagnosis except one but none had hypokalemia. All of them had mutation in the CYP17A1 gene. The two females responded well to oestrogen and progesterone and had adequate estrogenization clinically. Conclusions Even though CAH due to 17αOHD is quite rare, it should be considered while evaluating young individuals with hypogonadism, hypertension with or without hypokalemia. Lack of genital ambiguity and absence of classical signs at presentation does not rule out this not so uncommon condition and warrants follow up.

Meta-analysis of association between il-6-174 g/c polymorphism and female infertility related disorders

Female infertility continues to increase in prevalence annually and factors causing it need to be researched. As IL-6-174 G/C polymorphism is known to alter the plasma levels of IL-6, abnormal levels of IL-6 found in infertile females could be due to genetic reasons. With the understanding of the importance of IL-6 in reproductive physiology, several individual studies done so far to find the association of this polymorphism with female infertility related disorders were systematically combined for meta-analysis. Articles were searched using electronic data base sources and were included based on specific criteria. Finally, eight articles which includes polycystic ovarian syndrome (PCOS; n = 4), endometriosis (n = 3) and tubal damage (n = 1) were selected for the analysis. Results showed statistically significant heterogeneity across studies under the allele model (p < 0.0001, I² = 78 %) and dominant model (p < 0.00001, I² = 82%) but not under recessive model (p = 0.31, I² = 16%). This difference could be possibly due to variation in ethnicity, lifestyle, age or BMI related factors. The pooled odds ratio under the three genetic models were 0.87(CI = 0.75-1.02), 0.77 (CI = 0.63-0.94) and 1.05 (CI = 0.76-1.46) respectively. Sub group analysis showed statistical significant (P < 0.01) for PCOS under allele and dominant model, but not for endometriosis and tubal damage. By this meta-analysis, we can say that IL-6-174 G/C polymorphism can be considered as a potential genetic marker for PCOS but not for endometriosis and tubal damage disorders. However, more studies with adequate sample sizes are required to be done in endometriosis, tubal disease and other female infertility disorders to arrive at a definite conclusion.

Mutation Analysis Using Multiplex Ligation-Dependent Probe Amplification in Consanguineous Families in South India with a Child with Profound Hearing Impairment

BACKGROUND

Consanguineous marriage, a common practice in South India, increase the incidence of autosomal recessive diseases such as nonsyndromic hearing loss (NSHL) in offspring. This trend was noted in the children with hearing impairment (HI) who received cochlear implants (CI) at our University hospital in Porur, Chennai, India. To ascertain the genetic etiology of HI in these patients, we performed multiplex ligation-dependent probe amplification (MLPA) analysis.

METHODS

A total of 25 families who had a child with NSHL were included in the study. MLPA screening of GJB2, GJB6, and GJB3 was performed for all the recruited individuals.

RESULTS

The pathogenic p.W24X* mutation of GJB2 was detected in 2 patients; both of their parents were heterozygous carriers. Both families had a second-degree consanguineous marriage.

CONCLUSION

This study has important implications for molecular-diagnosis strategy and genetic counseling for families with HI in South India.

MicroRNA 146a Polymorphisms and Expression in Indian Children with Acute Lymphoblastic Leukemia

BACKGROUND

MicroRNAs (miR) have been reported to be involved in hematopoiesis and in the pathogenesis of several hematological malignant neoplasms. Single-nucleotide polymorphisms (SNPs) in human miR genes may alter the expression of those genes and influence the predisposition to childhood leukemia.

OBJECTIVE

To evaluate the association of rs2910164 G>C, rs57095329 A>G and the expression of miRNA-146a in ethnic South Asian children with acute lymphoblastic leukemia (ALL).

METHOD

Genotyping and expression analysis using TaqMan Small RNA Assay was performed on 71 patients with pathologically confirmed ALL and 74 control individuals.

RESULTS

No statistically significant association was found between the 2 SNPs, its expression levels, and ALL risk.

CONCLUSION

Haplotype analysis indicated a combination of allele A of rs57095329 and allele G of rs2910164 could represent a risk haplotype and an allele combination of G of rs57095329 and G of rs2910164 could represent a protective haplotype for ALL.

Evaluation of Cytogenetic Abnormalities in Patients with Acute Lymphoblastic Leukemia

Acute lymphoblastic leukemia (ALL) accounts for 20% of all adult leukemias and is the most common leukemia during childhood (80%). We present data on cytogenetics of ALL from a tertiary centre in India correlating it with clinical factors. Karyotyping of bone marrow samples of 204 patients with newly diagnosed ALL was performed with standard G-banding technique. Clinical data of patients was obtained from case records. Survival was estimated using Kaplan-Meir curves and compared by the log-rank test. Univariate and multivariate analysis was done for survival with age, sex, immunophenotype, hyperleukocytosis, risk type, remission status and cytogenetics. The most common karyotypes observed were normal in 39.7% (N = 81), hyperdiploidy in 12.7% (N = 26), t(9;22) in 4.4% (N = 9), t(1;19) in 3.9% (N = 8). Adults with ALL had worse survival compared with pediatric patients (HR 3.62; 2.03-6.45 95% CI, p < 0.001). Patients not in morphologic remission after induction chemotherapy fared poorly (HR 4.86; 2.67-8.84 95% CI, p < 0.001). Patients with favourable cytogenetics had better overall survival (HR 0.36; 0.12-1.05 95% CI, p < 0.05). On multivariate analysis, achievement of morphologic remission emerged as single most significant predictor of survival (p < 0.001). MLL gene rearrangement and t(12;21) were seen less commonly as compared to Western data. However, incidence rates of various cytogenetic abnormalities were similar to that reported from other centres from India. Age, morphologic remission at end of induction chemotherapy and favourable cytogenetics correlated significantly with survival.

A retrospective exploratory study of fetal genetic invasive procedures at a University Hospital

This is a retrospective analysis of the patient demographics and cytogenetic results of patients who underwent prenatal invasive testing for genetic analysis at the Foetal Medicine Division of the Department of Obstetrics and Gynecology, Sri Ramachandra Medical College and Research Institute. The main objective of this study was to characterise the changing trends in indications of pregnant women for foetal karyotyping in a 7-year period. A total of 257 procedures were performed in this period, and there was a significant change in the trend of indications for invasive prenatal diagnosis from an advanced maternal age in 2009 to a positive screen test by 2014. Chromosome abnormalities were observed in 9.8% of the cases, with trisomy 21 being the most frequent finding. The findings demonstrate the changing trends in screening and diagnostic testing in the tertiary care centre, with an acceptance of the first and second trimester maternal serum screening tests as a determinant for high-risk pregnancies. Impact statement What is already known on this subject? Despite the fact that India has one of the world's highest birth rates, there is still no public health care policy for the application of cytogenetic prenatal diagnosis. Nevertheless, we have been offering this test in our university teaching hospital since 2008, allowing us to characterise the changing trends in indications of pregnant women who sought invasive diagnostic procedures for foetal genetic studies. What do the results of this study add? The results of our study show that there were major changes in the common indications for prenatal diagnosis during the study period. In 2009, the main indication was an advanced maternal age, referred to in 31% of the cases, which declined steadily to 5% by 2014. In 2014, 51% of cases opted for a prenatal diagnosis because of a first trimester screen positive result, increasing from 12% in 2009. What are the implications of these findings for clinical practice and/or further research? This data is relevant as it would encourage other tertiary hospitals in developing countries like India to consider extending first trimester screening for all women, regardless of age and educate them on the options of prenatal genetic diagnosis for reassurance.

Differential expression of microRNAs let-7a, miR-125b, miR-100, and miR-21 and interaction with NF-kB pathway genes in periodontitis pathogenesis

Periodontitis is a chronic inflammatory disease which is caused by destruction of the tissues that surrounds and supports the tooth. Deregulation of microRNAs has been reported to cause several inflammatory diseases such as autoimmune disease, chronic periodontitis, and cancer. In the present study, we have investigated the expression pattern of microRNAs let-7a, miR-125b, miR-100, miR-21, and RNA-binding protein LIN-28A among healthy individuals and chronic periodontitis patients. Total RNA was isolated from gingival tissue samples collected from 100 healthy individuals and 100 chronic periodontitis patients. The expression of microRNAs and LIN-28 was performed by qPCR. Target prediction for the microRNAs was done using miRWalk and miRTarbase online databases and the experimentally validated targets were analyzed for their molecular function, biological processes, and related pathways using gProfiler software. The expression analysis revealed that let-7a and miR-21 were upregulated, whereas, miR-100, miR-125b, and LIN-28 were down regulated. The age dependent expression analysis revealed that the expression levels of all the microRNAs and LIN-28 were found to increase with age (more than 50 years), thereby suggesting an increased risk to chronic periodontitis. Among the various targets predicted using miRWalk and miRTarbase databases, NFKB was found to be a common target among all the four microRNAs. gProfiler revealed several functions such as NF-ĸB signaling pathway, cytokine-cytokine receptor interaction, osteoclast differentiation, etc., all of which specific to inflammation and periodontitis.

Subtelomeric rearrangements in Indian children with idiopathic intellectual disability/developmental delay: Frequency estimation & clinical correlation using fluorescence in situ hybridization (FISH)

Background & objectives:

Subtelomeres are prone to deleterious rearrangements owing to their proximity to unique sequences on the one end and telomeric repetitive sequences, which increase their tendency to recombine, on the other end. These subtelomeric rearrangements resulting in segmental aneusomy are reported to contribute to the aetiology of idiopathic intellectual disability/developmental delay (ID/DD). We undertook this study to estimate the frequency of subtelomeric rearrangements in children with ID/DD.

Methods:

One hundred and twenty seven children with idiopathic ID/DD were tested for subtelomeric rearrangements using karyotyping and FISH. Blood samples were cultured, harvested, fixed and GTG-banded using the standard protocols.

Results:

Rearrangements involving the subtelomeres were observed in 7.8 per cent of the tested samples. Detection of rearrangements visible at the resolution of the karyotype constituted 2.3 per cent, while those rearrangements detected only with FISH constituted 5.5 per cent. Five deletions and five unbalanced translocations were detected. Analysis of parental samples wherever possible was informative regarding the inheritance of the rearrangement.

Interpretation & conclusions:

The frequency of subtelomeric rearrangements observed in this study was within the reported range of 0-35 per cent. All abnormal genotypes were clinically correlated. Further analysis with array technologies presents a future prospect. Our results suggest the need to test individuals with ID/DD for subtelomeric rearrangements using sensitive methods such as FISH.

Reciprocal Microduplication of the Williams-Beuren Syndrome Chromosome Region in a 9-Year-Old Omani Boy

BACKGROUND

Microdeletions of the 7q11.23 Williams-Beuren syndrome chromosome region (WBSCR) are reported with a frequency of 1 in 10,000, whereas microduplications of the region, although expected to occur at the same frequency, are not widely reported.

METHOD

We evaluated a 9-year old Omani boy for idiopathic intellectual disability using genetic methods, including multiplex ligation-dependent probe amplification (MLPA), for detection of microdeletions (P064-B3).

RESULTS

MLPA analysis revealed that the boy has a rare microduplication of the WBSCR. Prominent clinical features include global developmental delay with pronounced speech delay, dysmorphic facies, and autistic features.

CONCLUSION

Microduplications, in general, are reported at a lesser frequency, perhaps owing to their milder phenotype. Complete genetic assessment in children with idiopathic intellectual disability would help in identifying rare conditions such as duplication of the WBSCR.

Prenatal Detection and Postnatal Follow-Up of Segmental Aneusomies of Chromosome 13 in 4 Consecutive Pregnancies in an Ethnic South Indian Family With a Maternally Inherited Balanced Translocation

OBJECTIVE

To assess the postnatal clinical manifestation of an antenatally detected unbalanced rearrangement involving chromosome 13 in an ethnic South Indian couple.

METHODS

We used conventional cytogenetics on fetal cells obtained from prenatal specimens and on peripheral blood lymphocytes from consanguineous family members to ascertain the chromosomal abnormalities.

RESULTS

We report the reproductive outcomes of a maternally inherited chromosome translocation involving chromosome 9 and 13 and the informed decisions of the couple, after genetic counseling in India, regarding their 4 pregnancies.

CONCLUSION

This case report highlights the current practice in India of offering prenatal diagnosis and preimplantation genetic diagnosis to individuals who are carriers of balanced translocations, to reduce the risk of conceiving chromosomally abnormal offspring.

Class II Analphoid Chromosome in a Child with Aberrant Chromosome 7: A Rare Cytogenetic Association

A neocentromere is a functional centromere that has arisen within a region not known to have a centromere. We present a case with a very rarely reported class II neocentromere formation in an aberrant chromosome 7. A 22-month-old male was referred because of dysmorphic features. Banding cytogenetics was performed, and a ring 7 and a supernumerary marker chromosome along with a normal chromosome 7 were found. In situ hybridization using a centromeric probe revealed 46 signals, of which 2 signals for chromosome 7 were observed, one on the normal and one on the ring chromosome. Further analysis using FISH revealed that the linear acentric fragment was part of the 7q region, which suggests that there could be a possible McClintock mechanism.

Isolation and evaluation of cytogenetic effect of Brahmi saponins on cultured human lymphocytes exposed in vitro

Major saponins of Brahmi (Bacopa monniera, Fam: Scrophulariaceae) - bacosides A and B - were isolated from the total methanol extract and characterised based on melting point, TLC, IR, (1)H NMR and (13)C NMR. They were evaluated for their in vitro cytogenetic effects on human peripheral blood lymphocytes by chromosomal aberration (CA) assay and sister chromatid exchange (SCE) assay. The frequency of chromatid type aberrations and reciprocal interchanges between sister chromatids in the treated cells was scored in comparison to the untreated control. At 30 μg/mL dose, bacoside A showed a statistically significant increase in the frequency of both CA and SCE and bacoside B showed an increase only in SCE. Our report of the genotoxicity of the saponins is significant in view of the reports of anticancer activity of Brahmi extracts.

Recurrence of Angelman syndrome in siblings: challenges in genetic counseling

The authors report a rare occurrence of two siblings with Angelman syndrome. Their karyotype revealed monosomy of chromosome 15 and a derivative chromosome 1 leading to Angelman syndrome. Their mother was a balanced translocation carrier involving chromosomes 1p and 15p. In her subsequent pregnancy, prenatal karyotype analysis was offered and the fetus was unaffected.

Klinefelter's syndrome (mosaic) with chromosome 9 inv and schizophrenia

Klinefelter's syndrome is a sex chromosome abnormality with low androgen level. The varied manifestations of the mental symptoms in some of them, that are inexplicable based on their genotype alone, has fascinated the researchers. We present here a case of Klinefelter's syndrome having a karyotype of mos 47, XXY, and also inversion in 9(th) chromosome, with schizophrenia. Despite the view that inv 9 is a normal variant, it is still worthwhile to explore whether it has any role in the etiology of schizophrenia especially when it occurs with other genotypic aberrations that are suspected to have relevance to psychiatric disorders including the Klinefelter's syndrome.

Coronary Artery Disease in Patients Aged 35 or less - A Different Beast?

Aim:

To assess the extent and severity of coronary artery disease (CAD) in 200 consecutive patients aged 35 years or less undergoing diagnostic coronary angiography.

Patients and Methods:

Findings in these 200 patients (≤ 35 years of age) were analyzed to find the extent and severity of CAD. The mean age was 31.69 (±3.76) years. Majority were males (94%) and from the Arab ethnicity (70.5%).

Result:

Smoking (71%) and history of premature CAD (27%) were the most frequent risk factors (RF). History of previous ST elevation myocardial infarction (MI) was present in 68%. Anterior wall MI was the most frequent location (63.3%). The majority (54.3%) had moderate or large size MI. Ejection fraction (EF) less than 50% was noted in 30.3%. Left main or triple vessel CAD was seen in 15%. One- and two-vessel CAD was seen in 32.5% and 19% patients, respectively. Coronary angiogram was completely normal in 23.5%. The majority (54.5%) were treated conservatively and the rest (45.5%) needed percutaneous coronary intervention (PCI) or coronary artery bypass graft (CABG). The mean number of stents used was 1.3 ± 0.67 and the mean length of stents used was 20.3 ± 12.6 mm.

Conclusion:

The extent and severity of CAD was very significant in this subgroup of very young (≤35 years) Asian patients. Smoking was the main risk factor and half of the patients needed either PCI or CABG.

A de novo reciprocal t(2;18) translocation with regular trisomy 21

A 4-year-old girl with Down syndrome exhibited an autosomal translocation t(2;18) in addition to trisomy 21. An evaluation of GTG-banded metaphases revealed the karyotype 47,XX,t(2;18),21 that was confirmed by using fluorescent in situ hybridization (FISH) probes. This case represents a very rare coincidence of an autosomal aneuploidy and a structural rearrangement. Her parents showed a normal chromosome complement. The translocation must have been an apparently "balanced" one as the proband presented with typical features of Down syndrome alone. The mechanism of origin of this rearrangement along with a nondisjunctional error and its significance are discussed.