Dependent Probe Amplification Research Articles

The application of chromosomal microarray analysis to the prenatal diagnosis of isolated mild ventriculomegaly

ObjectiveTo investigate the clinical value of chromosomal microarray analysis (CMA) in the prenatal diagnosis of genetic abnormalities in fetal isolated mild ventriculomegaly. Materials and methodsThis retrospective study reviewed 101 fetuses with isolated mild ventriculomegaly who had undergone invasive prenatal diagnosis at our hospital. CMA was performed in all cases to detect chromosomal aneuploidy as well as copy number variations (CNVs) that are too small to be detected by conventional karyotyping. Real time quantitative PCR (qPCR) or multiplex ligation dependent probe amplification (MLPA) was used to confirm all fetal CNVs <400 Kb. ResultsExcept for three cases of chromosomal aneuploidy, CMA revealed pathogenic copy number variations (CNVs) in 3.0% (3/101) of the fetuses; these cases demonstrated involvement in the chromosomal regions 15q11.2, 1q21.1 and Xq27.3q28. Furthermore, we detected three likely pathogenic (3.0%) and two variants of uncertain significance (2.0%) among 101 fetuses diagnosed as isolated mild ventriculomegaly on ultrasound examination. ConclusionOur study suggests that CNVs could aid in the risk assessment and genetic counseling in fetuses with isolated ventriculomegaly.

Diagnostic value of multiplex ligation dependent probe amplification combined with Sanger sequencing in 21-hydroxylase deficiency

Objective: To study the procedure of CYP21A2 gene mutation detection in 21-hydroxylase deficiency (21-OHD) patients. Methods: The detail clinical and biochemical data of 51 patients with 21-OHD [18 males and 33 females, with an average age of (16.4±9.9) years] were collected between December 2016 and December 2017 at Department of Endocrinology, Peking Union Medical College Hospital. Multiplex ligation dependent probe amplification (MLPA) and Sanger sequencing of the CYP21A2 gene were used to clarify the cause of 21-OHD. The genotype-phenotype correlation was also analyzed. Results: The incidences of large deletion, 8 bp deletion, I2G, I172N and F306+T were 19.6% (20/102), 1.0% (1/102), 30.4% (31/102), 25.5% (26/102) and 1.0%(1/102), respectively, and the detection rate of gene mutation in 51 21-OHD patients was 77.5% (79/102) by MLPA test. Except large and 8 bp deletion, all above mutations contained in MLPA and other 8 mutations, including P31L, Q319X, R361L, R357W, V282L, R484Q, G425S and R342W were detected, and the detection rate was 79.4% (81/102) by Sanger sequencing of CYP21A2. MLPA combined with direct sequencing identified mutations in all patients. Genotype correlated well with clinical phenotype in 21-OHD patients. Conclusions: When MLPA or CYP21A2 gene sequencing were used alone to diagnose the cause of 21-OHD, gene mutations in all patients could not be detected. The combination of the two methods can complement each other and fully clarify the underlying causes of 21-OHD.

Newborn screening for Prader-Willi syndrome is feasible: Early diagnosis for better outcomes.

Prader-Willi syndrome (PWS), is a complex genetic disease affecting 1/15,000 individuals, characterized by lack of expression of genes on the paternal chromosome 15q11-q13 region. Clinical features include central hypotonia, poor suck, learning and behavior problems, growth hormone deficiency with short stature, hyperphagia, and morbid obesity. Despite significant advances in genetic testing, the mean age for diagnosis in PWS continues to lag behind. Our goal was to perform a pilot feasibility study to confirm the diagnosis utilizing different genetic technologies in a cohort of 34 individuals with genetically confirmed PWS and 16 healthy controls from blood samples spotted and stored on newborn screening (NBS) filter paper cards. DNA was isolated from NBS cards, and PWS testing performed using DNA methylation-specific PCR (mPCR) and the methylation specific-multiplex ligation dependent probe amplification (MS-MLPA) chromosome 15 probe kit followed by DNA fragment analysis for methylation and copy number status. DNA extraction was successful in 30 of 34 PWS patients and 16 controls. PWS methylation testing was able to correctly identify all PWS patients and MS-MLPA was able to differentiate between 15q11-q13 deletion and non-deletion status and correctly identify deletion subtype (i.e., larger Type I or smaller Type II). mPCR can be used to diagnose PWS and MS-MLPA testing to determine both methylation status as well as the type of deletion or non-deletion status from DNA extracted from NBS filter paper. We propose that PWS testing in newborns is possible and could be included in the Recommended Uniform Screening Panel after establishing a validated cost-effective method.

Profile of Mutations Identified in the 3WINTERS-IPS Project on European & Iranian Patients with Previously Diagnosed Type 3 Von Willebrand Disease.

Profile of Mutations Identified in the 3WINTERS-IPS Project on European & Iranian Patients with Previously Diagnosed Type 3 Von Willebrand Disease.

Deletions in SERPING1 Lead to Lower C1 Inhibitor Function: Lower C1 Inhibitor Function Can Predict Disease Severity

Background: How genotype affects phenotype in hereditary angioedema with C1 inhibitor deficiency (C1-INH-HAE) has not been totally clarified. In this study, we investigated the relationship between different types of mutations and various phenotypic characteristics. Methods: Clinical data from 81 patients from 47 families were recorded. Complement proteins were analyzed from 61 untreated patients. The coding exons and the exon-intron boundaries of the SERPING1 gene were sequenced, and deletion/duplication analysis with multiple ligation dependent probe amplification was performed. The relationship of complement protein with the mutation type was analyzed by using generalized estimating equations. Results: Thirty-five different mutations (15 novel and 2/15 homozygous) were identified. There was no causative mutation in 6 patients (7.4%). Patients with deletion and large deletion had the lowest (5.05%, 0–18.7; 5.8%, 0–16.5%, respectively), and the none mutation group had the highest C1 inhibitor function (23.3%, 11–78%, p < 0.001). C1 inhibitor function levels decreased as the age of the disease progressed (r = –0.352, p = 0.005). Lower C1 inhibitor function levels caused severer disease (r = –0.404, p = 0.001) and more frequent annual attacks (r = –0.289, p = 0.024). In the off-attack period, C1q levels were lower than normal in 9.8% of the patients. Conclusion: Deletion mutations may represent the most unfavorable effect on C1 inhibitor function. The earlier disease onset age could be a sign for lower C1 inhibitor function levels in adult life. C1q levels could also be low in C1-INH-HAE patients, as in acquired angioedema. Lower C1 inhibitor function can predict disease severity and may have negative impacts on the course of C1-INH-HAE.

Multiplex ligation dependent probe amplification - A useful, fast and cost-effective method for identification of small supernumerary marker chromosome in children with developmental delay and congenital heart defect

Abstract Small supernumerary marker chromosome (sSMC) is a rare chromosomal abnormality and is detected in about 0.3% in cases with multiple congenital anomalies (MCA) and/or developmental delay. Different techniques for investigation of cases with MCA and/or developmental delay are available ranging from karyotyping to molecular cytogenetic technique and ultimately multiplex ligation dependent probe amplification (MLPA). Here we present a patient with multiple congenital anomalies for which classical cytogenetic technique was used as a first step in diagnosis and the results being confirmed by MLPA. The karyotype disclosed a sSMC considered to be a fragment of chromosome 22. The MLPA analysis using SALSA MLPA probemix P064-C2 Microdeletion Syndromes-1B confirmed the karyotype results, and according to the manufacturer’s recommendation we performed another confirmation analysis with MLPA probemix P311-B1 Congenital Heart Disease and MLPA probemix P250-B2 DiGeorge. We also suspected an Emanuel syndrome and performed another MLPA analysis with SALSA MLPA probemix P036-E3 Subtelomeres Mix 1 and probemix P070-B3 Subtelomeres Mix 2B for investigation of subtelomeric region that revealed a duplication of 11q25 region and the confirmation was performed using SALSA MLPA probemix P286-B2 Human Telomere-11. In conclusion, we consider that MLPA is a valuable method for identification of sSMC in children with developmental delay and congenital anomalies. Genetic diagnosis using different molecular techniques, such as MLPA, for increasing accuracy in identification of chromosomal structural aberrations has an important role in clinical diagnosis and in genetic counselling and our case explain the importance of using a specific laboratory technique for each stage of diagnosis.

Novel gross deletion at the GHRHR gene locus possibly mediated by Alu specific microhomology identified in a Sri Lankan patient with isolated growth hormone deficiency

ObjectiveCharacterization of a deletion in the exon 1 and 5′ regulatory region of the GHRHR gene in a proband with isolated growth hormone deficiency. MethodsMultiple ligation dependent probe amplification (MLPA) assay was carried out to confirm the homozygous deletion which was suspected during screening of the GHRHR gene by single strand conformation polymorphism. A series of short range PCR amplifications were carried out to map the approximate location of the break points of the deletion. Sanger sequencing was carried out to locate the break points and to identify the length of the deletion. Long range PCR amplification was carried out to confirm the length of the deletion and to screen the parents of the proband for the deletion. ResultsA homozygous deletion was confirmed via MLPA assay. Zones of sequence similarity between upstream intergenic region and intron 1 of the GHRHR gene were identified. Break points of the deletion were identified within perfectly matching 32 bp repeat sequences ie: microhomologies in the specified zones. The novel deletion may have arisen via Alu specific microhomology mediated non-recurrent rearrangement in the maternal lineage of the proband. The deletion being reported in this study include, last 3118 bp from the upstream intergenic region and complete exon 1 and first 2620 bp from intron 1 and one of the 32 bp microhomologies. The total length of the deleted segment was 5875 bp. As the deleted region contained significant elements essential for gene expression, the identified deletion is being reported as likely pathogenic. The same deletion was identified in the mother in heterozygous state. ConclusionWe have characterized a novel deletion that seems to have arisen via Alu specific microhomology mediated non-recurrent rearrangement at GHRHR gene locus. HGVS nomenclature of the deletion is c.-3166_58-2057del. This novel structural variant was identified to be the cause of IGHD of the affected proband.

Detecting 22q11.2 Deletion Syndrome in Newborns with Low T Cell Receptor Excision Circles from Severe Combined Immunodeficiency Screening

Based on experiences and results from newborn screening for severe combined immunodeficiency (SCID), we evaluated the occurrence of chromosome 22q11.2 deletion syndrome (22q11.2DS) in newborns with different T cell receptor excision circles (TREC) results and established a second tier genetic test for 22q11.2DS. Recalled dried blood spots from 486 newborns with TREC results <90 copies/uL were tested from the SCID newborn screening. Quantitative real-time polymerase chain reaction assay was used to detect the copy number of TBX1 and HIRA genes by simple DNA extraction method. Multiplex ligation dependent probe amplification was used for further confirmation. Four hundred sixty-eight cases were considered negative because their haploid copy number of TBX1 and HIRA genes was >0.75. Eighteen cases with TBX1 and/or HIRA gene copy number <0.75 were suspected as positive, and 13 cases were further confirmed with 22q11.2DS. Detection rates of 22q11.2DS were 10.7% (6/56) in TREC <30 copies, 6.8% (9/132) in <50 TREC copies, 4.6% (12/260) in <70 TREC copies, and 2.7% (13/486) in <90 TREC copies. 22q11.2DS detection can be incorporated into the second-tier assay in subjects with low TREC copies in SCID screening. The dried blood spot methods were feasible for 22q11.2DS newborn screening.

Mutation analysis of the autosomal dominant Weill-Marchesani syndrome and genotype-phenotype review

Objective To screen the disease-causing genes in an autosomal dominant(AD)Weill-Marchesani syndrome (WMS) family from Henan province in China, and to analyze the relationship between genotypes and phenotypes of the AD WMS. Methods A family with suspected WMS was collected and studied in Henan Eye Hospital from September 2016 to July 2017.Clinical data and genomic DNA of the families were analyzed and genetic variations were screened by whole-exome sequencing (WES) The candidate genes related to ectopia lentis (FBN1, ADAMTSL2, ADAMTSL4, TGFBR2, CBS, ADAMTS10, ADAMTS17) were analyzed, and multiplex ligation dependent probe amplification (MLPA) was applied.Novel variants were further evaluated by sequencing 96 normal individuals.The previous reports with similar genetic characteristics were reviewed and the mutation types and clinical features were summarized.Written informed consent was obtained from the participants or their guardians before the collection of their venous blood and clinical data.Ethical approval was obtained from the Institutional Review Board of Henan Eye Institute. Results The suspicious mutation of the c. 5260G>A was detected in exon 42 of the FBN1 by WES in this family, which was predicted to be pathogenic and cosegregated with the disease; the clinical futures of the patients in the family included proportionate short stature, brachydactyly, joint stiffness, and the ocular problems included microspherophakia, moderate myopia, secondary glaucoma.Four mutations of FBN1 that related to WMS were reported in previous literature, and three of them were located in 41-42 exons and the others were the deletion of exons 9-11.All patients had typical clinical features of microspherophakia, short stature, brachydactyly, joint stiffness.In addition, thick skin was common, heart defects were occasional, protuberant abdomen and umbilical hernia were rarely reported. Conclusions The affected members in this family are in according with the clinical and genetic diagnosis of WMS.A novel mutation (c.5260G>A) in FBN1 is discovered, which increases the spectrum of WMS mutation.The 41-42 exons of the FBN1 are hotspot of mutation in WMS. Key words: Weill-Marchesani syndrome; FBN1 gene; Whole-exome sequencing; Phenotype

PO-016 The role of autophagy-related protein 9B in liver carcinogenesis

IntroductionAccording to the National Cancer Register in Bulgaria more than 800 women develop ovarian cancer annually. The most frequent histological type, representing about three quarters of these cases is high-grade serous ovarian carcinoma (HS-OC). About 25% of the HG-OC are supposed to be caused by mutations in the BRCA1 and BRCA2 genes.Material and methodsWe have screened 80 Bulgarian patients with high grade serous ovarian cancer (HS-OC), disease progression and platinum sensitivity for germline mutations in the BRCA1/2 genes. The mutation analysis was performed by Next Generation Sequencing (NGS) with Ion Torrent PGM System, Sanger Sequencing and MLPA (Multiplex Ligation Dependent Probe Amplification). All identified pathogenic variants with NGS were confirmed by direct sequencing.Results and discussionsIn total 26 (32.5%) pathogenic mutations were found of which 23 (28.75%) in BRCA1: three recurrent c.5263_5264insC (7/80), c.2019delA (3/80), c.5333–1G>A (2/80), the rest appearing just once c.139T>C, c.139T>G, c.181T>G, c.3496delG, c.4391delC, c.5212G>A, c.5497G>A, c.5533_5534insT, deletion of exons 3–7. In BRCA2 only 4 (5%) mutations were found: c.3545_3546delTT, c.8059_8063delGTTCT, c.8674A>T, c.9294C>G. The most prevalent mutation in the study group observed with frequency of 8.75% was c.5263_5264insC, followed by c.2019delA (3.75%) and c.5333–1G>T (2.50%) in BRCA1. The recurrent mutations account for 57.7% of all detected mutations.ConclusionTwenty six (32.5%) of the HS-OC patients in our study were carriers of germline pathogenic mutations. These results are relevant to the clinical practice and personalised treatment of patients with OC. The BRCA1 and BRCA2 mutations are related to survival and chemotherapy response. The mutation carriers, detected by NGS sequencing, could benefit from therapy with PARP inhibitor.AcknowledgementsDUNK01-2/2009/NSF, Ministry of Education and Science, Bulgaria, AstraZeneca LTD, Bulgaria

Frequency of BRCA1 Mutations in B&amp;H Breast and Ovarian Cancer Patients

Incidence of breast cancer ranges from 27 per 100,000 in Middle Africa and Eastern Asia to 92 per 100,000 in Northern America. It is the fifth most common cause of death from cancer in women, with an estimated 522,000 deaths per year (6.4% of the total). Autosomal dominant inheritance of these cancers is characterized by transmission of cancer predisposition from generation to generation, with around 5-10% of all breast cancers being associated with inherited mutations in BRCA1, BRCA2 and other genes. Breast and ovarian cancers are strongly associated with BRCA1 and BRCA2 mutations. In this study, we genotyped BRCA1 gene for large genomic rearrangements in breast and ovarian cancer patients from Bosnia and Herzegovina, with aim to assess frequency of large BRCA1 mutations (exon deletions/duplications) in this group. We collected 59 breast cancer samples, as well as other data concerning patients’ histopathological parameters of tumor, like age at diagnosis, cancer type, TNM class, cancer grade, as well as estrogen, progesterone and Her2/neu expression. Following DNA extraction from breast cancer samples (tissue after biopsy), BRCA1 mutations were identified by Multiplex Ligase - Dependent Probe Amplification (MLPA) analysis. Biostatistical analyses were conducted using MedCalc v.9.2.0.0 software. In all statistical tests p&lt;0.05 was considered significant. Mean age at diagnosis was 54±1.75 (range 17 – 80). BRCA1 genomic rearrangements were found in 22% of breast and ovarian cancer patients. Statistically significant associations and correlations were found between BRCA1 genomic rearrangements and cancer type, estrogen, progesterone and Her2/neu expression, but not cancer grade, size, invasiveness or patients’ age.

Mutational analysis in patients with Autosomal Dominant Polycystic Kidney Disease (ADPKD): Identification of five mutations in the PKD1 gene

Autosomal Dominant Polycystic Kidney Disease (ADPKD), the most frequent genetic disorder of the kidneys, is characterized by a typical presenting symptoms include cysts development in different organs and a non-cysts manifestations. ADPKD is caused by mutations in PKD1 or PKD2 genes. In this study, we aimed to search for molecular causative defects among PKD1 and PKD2 genes. Eighteen patients were diagnosed based on renal ultrasonography and renal/extra-renal manifestations. Then, Sanger sequencing was performed for PKD1 and PKD2 genes. Multiplex Ligation dependent Probe Amplification method (MLPA) methods was performed for both PKD genes. Mutational analysis of the PKD2 gene revealed the absence of variants and no deletions or duplications of both PKD genes were detected. But three novels mutations i.e. p.S463C exon 7; c. c.11156+2T>C IVS38 and c.8161-1G>A IVS22 and two previously reported c.1522T>C exon 7 and c.412C>T exon 4 mutations in the PKD1 gene were detected. Bioinformatics tools predicted that the novel variants have a pathogenic effects on splicing machinery, pre-mRNA secondary structure and stability and protein stability. Our results highlighted molecular features of Tunisian patients with ADPKD and revealed novel variations that can be utilized in clinical diagnosis and in the evaluation of living kidney donor. To the best of our knowledge, this is the first report of Autosomal Polycystic Kidney Disease in Tunisia.

Molecular Testing of MECP2 Gene in Rett Syndrome Phenotypes in Indian Girls

To assess yield of MECP2 gene sequence variations analysis and large deletions in suspected cases of Rett syndrome. Descriptive study. Tertiary-care medical genetics center. Girls with neuroregression, postnatal microcephaly and signs and symptoms suggestive of classical and atypical Rett syndrome were classified into two groups. Group I consisted of girls with Classical and atypical Rett syndrome on basis on the Revised Rett Syndrome diagnostic criteria, 2010. Group II included girls with neuroregression and postnatal microcephaly and other Rett like features but not fulfilling the above criteria. Sanger sequencing of coding regions and large deletional analysis of MECP2 gene. Identification of mutation in MECP2 gene. Mutation in MECP2 gene was identified in 74% (14/19) in group I and none (0/17) in group II. The mutation detection rate was 93% (13/14) in group I classical Rett syndrome girls (2 with large deletions identified with Multiplex ligation dependent probe amplification) and 20% (1/5) in group I atypical Rett syndrome girls. One novel MECP2 sequence variation was identified in group I classical Rett syndrome. The yield of the mutation detection in MECP2 is higher in classical Rett syndrome. In girls with some Rett like features, but not fulfilling revised Rett syndrome diagnostic criteria, mutation testing for MECP2 gene has a low yield.

Duplication of SOX9 associated with 46,XX ovotesticular disorder of sex development.

The purpose of the present study was to investigate whether ten unrelated SRY-negative individuals with this sex differentiation disorder presented a double dose of SOX9 as the cause of their disease. Ten unrelated SRY-negative 46,XX ovotesticular disorder of sexual development (DSD) subjects were molecularly studied. Multiplex-ligation dependent probe amplification (MLPA) and quantitative real-time PCR analysis (qRT-PCR) for SOX9 were performed. The MLPA analysis demonstrated that one patient presented a heterozygous duplication of the entire SOX9 coding region (above 1.3 value of peak ratio), as well as at least a ~ 483 kb upstream duplication. Moreover, no duplication of other SOX9 probes was observed corresponding to the region between -1007 and -1500 kb upstream. A qRT-PCR analysis showed a duplication of at least -581 kb upstream and ~1.63 kb of the coding region that encompasses exon 3. The limits of the duplication were mapped approximately from ~71539762 to 72122741 of Chr17. No molecular abnormalities were found in the remaining nine patients. This study is thought to be the first report regarding a duplication of SOX9 that is associated with the presence of 46,XX ovotesticular DSD, encompassing at least -581 kb upstream, and the almost entire coding region of the gene.

Loss of heterozygosity (LOH) Analysis in individuals with developmental delay/congenital anomalies previously investigated for 22q11.2 Deletion Syndrome

LLoss of heterozygosity (LOH) also called absence of heterozygosity (AOH) or regions of homozygosity (ROH) can be detected by SNP-array analysis. It is observed in regions identical by descent or occurs because of errors in the mechanisms of recombination between homologous chromosomes, DNA replications or DNA repair. The 22q11.2 deletion syndrome (22q11.2DS) has a prevalence of 1/4000 live births and an extensive clinical variability. About 30% of individuals with 22q11.2DS clinical suspicion have been diagnosed with the typical 22q11.2 deletion and other genomic imbalances are often reported related to similar phenotypes. However, most of patients remain without an etiological diagnosis. Currently, there are few studies about LOH in individuals with developmental delay/congenital anomalies. The aim of this study is to describe the preliminary results of LOH analysis in individuals with clinical suspicion of 22q11.2DS. Inclusion criteria was individuals with clinical suspicion without the typical 22q11.2 deletions, previously tested by Fluorescent in situ Hybridization (FISH) or Multiplex Ligation Probe-dependent Amplification (MLPA). Exclusion criteria was parental consanguinity. A total of 124 individuals were investigated by chromosomal microarray analysis (CMA) using the CytoScan HD or 750K Array (Affymetrix®). Data were compared with a database composed by 114 control individuals from Brazilian general population. We considered only LOH biggest than 3Mb and not frequent (&lt;1%) in control individuals. The presence of LOH was more often in the patients than in the control group (12,1% against 3,5%). In the patient group the LOH size were between 3,3Mb and 46,2Mb (average size 22,7Mb) and in the control group it was between 3,1Mb and 8,5Mb (average size 6,0Mb). It was observed only one large LOH for almost all patients, and for almost all the control group it was observed two small LOHs. Among patients with LOH, six also carried VOUS (variants of uncertain significance) and one had a pathogenic imbalance. Laboratorial confirmations and genotype-phenotype correlation are in progress. Our results clearly show a higher proportion and bigger size of LOHs in individuals with developmental delay/congenital anomalies and a possible applicability of LOH analysis as a diagnostic approach in individuals with the same characteristics of the present sample.Support: Fapesp and CNPq

Cyclin dependent kinase inhibitor 2A/B gene deletions are markers of poor prognosis in Indian children with acute lymphoblastic leukemia.

Cyclin dependent kinase inhibitor 2A/B (CDKN2A/B) genes are implicated in many malignancies including acute lymphoblastic leukemia (ALL). These tumor suppressor genes, with a key regulatory role in cell cycle are located on chromosome 9p21.3. Previous studies involving CDKN2A/B gene deletions have shown mixed associations with survival outcome in childhood ALL. Hundred and four newly diagnosed children with ALL (1-14 years) were enrolled in this study. Genomic DNA from pretreatment bone marrow/peripheral blood samples of these children was investigated for copy number alterations in CDKN2A/B genes using multiplex ligation dependent probe amplification assay. Immunophenotype subtyping and cytogenetic and molecular analysis of ALL was performed at start of induction chemotherapy in all children. Children were monitored for response to prednisolone (Day 8), complete morphological remission, and minimal residual disease at the end of induction. The minimum postinduction follow-up period was 6 months. CDKN2A/B deletions were seen in 19.8% (18/91) of B lineage acute lymphoblastic leukemia (B-ALL) and 38.5% (5/13) of T lineage acute lymphoblastic leukemia (T-ALL). Monoallelic CDKN2A/B deletions were found in 61.1% of total deletions in B-ALL while all the children with T-ALL harbored biallelic deletions. The prevalence of CDKN2A/B gene deletions was found to be significantly higher in older children (P=0.002), in those with higher leukocyte count (P=0.037), and in National Cancer Institute high risk group patients (P=0.001) in the B-ALL subgroup. Hazard ratio was significantly high for children with CDKN2A/B deletions in total cohort (P=0.004). Children with CDKN2A/B deletion had significantly lesser event free survival (P=0.03). CDKN2A/B deletions were significantly more prevalent in T-ALL subgroup and were found to have higher hazard ratio and lesser event free survival in total cohort in our study.

High frequency of intermediate and poor risk copy number abnormalities in pediatric cohort of B-ALL correlate with high MRD post induction

Copy number abnormalities (CNAs) and recurrent fusion transcripts are important genetic events which define and prognosticate B-Cell Acute Lymphoblastic Leukemia (B-ALL). We evaluated CNAs and fusion transcripts in 67 pediatric B-ALL cases and correlated the data with standard risk factors and early treatment outcome parameters. Common fusion transcripts ETV6-RUNX1, E2A-PBX, BCR-ABL1 and MLL-AF4 were examined by RT-PCR and noted in 15%, 15%, 13% and 1.4% of all cases respectively. CNAs in IKZF1, PAX5, EBF1, BTG1, RB1, CDKN2A/B and genes from PAR1 region viz., CSF2RA, IL3RA,P2RY8, SHOX region and CRLF2 were analyzed by multiplex ligation dependent probe amplification assay and were detected in 70% (47/67) of cases, with predominantly deletions in CDKN2A/B (36%), PAX5 (18%) and IKZF1 (16%). A statistically significant association of intermediate/poor risk CNAs was noted with high WBC count (p = 0.001), NCI group (p = 0.02) and minimal residual disease at Day35 (p < 0.0001). IKZF1 and CDKN2A/B deletion revealed poor EFS of 56% at 24 months as compared to EFS of 80% in rest of the cases (p = 0.05) suggesting their potential role in early risk stratification.

Novel noncontiguous duplications identified with a comprehensive mutation analysis in the DMD gene by DMD gene-targeted sequencing

Genomic rearrangements, such as intragenic deletions and duplications, are the most prevalent types of mutation in the DMD gene, and DMD mutations underlie Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD). Using multiplex ligation dependent probe amplification (MLPA) and DMD gene-targeted sequencing, we performed a molecular characterization of two cases of complex noncontiguous duplication rearrangements that involved inverted duplications. The breakpoint sequences were analyzed to investigate the mechanisms of the rearrangement. The two cases shared the same duplication events (Dup-nml-Dup/inv), and both involved microhomology and small insertions at the breakpoints. Additionally, in case 1, SNP sequencing results indicated that the de novo duplication mutation arose in the allele that originated from the grandfather. This study has identified a novel type of DMD complex rearrangement and provides insight into the molecular basis of this genomic rearrangement.

Improving clinical diagnosis in SHOX deficiency: the importance of growth velocity.

BackgroundThe aim of this study was to estimate the prevalence of haploinsufficiency of short stature homeobox containing gene (SHOX) deficiency (SHOXD) in a population of short-statured children, and to analyze their phenotype and the performance of clinical scores.MethodsScreening for SHOXD was performed in 281 children with short stature by direct sequencing and multiplex ligation probe-dependent amplification. Subjects with SHOXD were compared with 117 matched short patients without SHOXD. We calculated the cutoff of growth velocity associated with the highest sensitivity and specificity as a screening test for SHOXD by receiver operating characteristic curves.ResultsThe prevalence of SHOXD was 6.8%. Subjects with SHOXD showed a lower growth velocity (P<0.05) and a higher prevalence of dysmorphic signs. The best cutoff for growth velocity was -1.5 standard deviation score (SDS) both in the whole population and in subjects with a Rappold score <7 and <4 points. Growth velocity was ≤-1.5 SDS or Rappold score was >7/>4 points in 17/17 of 19 children with SHOXD and in 49/65 of 117 subjects without SHOX mutations.ConclusionsGrowth rate ≤-1.5 SDS, even with negative Rappold score, may be useful to detect precociously children with SHOXD. Selecting children deserving the genetic test by using growth velocity or the Rappold score significantly increases the sensitivity in detecting mutations and decreases the specificity.

Analysis of SMN1 gene mutations in 78 patients with spinal muscular atrophy

To explore the significance of SMN1 gene mutations among patients with spinal muscular atrophy (SMA) and the value of multiplex ligation dependent probe amplification (MLPA) for its diagnosis. Potential mutations of the SMN1 gene were detected among 78 SMA patients with a MLPA assay. Homozygous deletion of SMN1 exons 7 and 8 was detected in 70 (89.7%) of all patients. Homozygous deletion of exons 7 and heterozygous deletion of exon 8 was detected in 3 patients (3.8%). Homozygous deletion of SMN1 exons 7 alone was detected in 3 patients (3.8%). Heterozygous deletion of SMN1 exons 7 and 8 was detected in 2 patients (2.6%). For 77 of the patients, both parents were found to carry heterozygous deletion of the SMN1 gene, which was consistent with the recessive inheritance of SMA. One patient with SMA type I was found to be rather rare. The patient was found to carry homozygous deletion of SMN1 exons 7 and 8, for which her mother was heterozygous, while no mutation was found in her father. Homozygous deletion of the SMN1 gene have been detected in more than 95% of SMA patients. No homozygous deletion of exon 8 has been found. Homozygous deletion of exon 7 is more significant in the pathogenesis of SMA.